docs: name bin/brain/search.go; --hop is not a graph walk. (#10)

Published docs and skills still taught bin/kb/search --hop 1. Search lives
at bin/brain/search.go; --hop errors until File edges exist. A unittest
gates the SoT so the lie cannot return.

AGENTS.md

@@ -36,14 +36,10 @@ PLAN.md       decisions + execution + open questions
 docs/         published docs
 skills/       in-project agent skills (vendored, no external links)
 bin/          self-describing tools bin/{subject}/{method}.go (shebang)
-bin/brain/    search.go serve.go index.go get.go stats.go eval.go watch.go
-bin/chats/    sync.go import.go facts.go apply.go; libs in internal/chats
-bin/mail/     sync.go import.go (index_mail → brain/index.go)
-bin/markdown/ import.go (mistune leafs)
-bin/postgres/ query.go (read-only YAML)
-bin/git/      import.go (go-git history; Python shim execs it)
-internal/     shared Go (brain/rank is cgo-free; chats parsers; gitlog)
-bin/watch/    corpus watcher (used by bin/brain/watch.go)
+bin/brain/    search.go, serve.go; libs in internal/brain and internal/httpapi
+internal/     shared Go (brain/rank is cgo-free)
+bin/watch/    corpus watcher (internal via bin/brain/watch later)
+bin/mail/     mail pipeline: sync (Go), import (md), index_mail (rebuild)
 bin/tools/    vendored python libs behind bin/* (kblib, yamlout, websearch)
 bin/docker-entrypoint  container entrypoint (brain index|search|serve|watch)
 compose.yaml  docker composition (root level, not docker/)
@@ -57,8 +53,8 @@ var/          kb.lbug, var/mail/*, caches (gitignored)
 ```bash
 bin/mail/sync.go --source onlyoffice,gmail --workers 8 --out var/mail   # raw message.json + attachments
 bin/mail/sync.go --source gmail --query 'from:example.com' --out var/mail  # Gmail search (default in:inbox)
-bin/mail/import.go --from-raw var/mail                                  # message.json → message.md (convert only)
-bin/brain/index.go --rebuild                                            # rebuild brain incl. all mail (fresh DB)
+bin/mail/import --from-raw var/mail                                     # message.json → message.md (convert only)
+bin/mail/index_mail                                                     # rebuild brain incl. all mail (fresh DB)
 ```
 
 - `sync` (Go) downloads messages + attachments; Gmail uses paginated list +
@@ -67,7 +63,7 @@ bin/brain/index.go --rebuild                                            # rebuil
   `pdftotext -layout` fast path (~15ms); textless/scanned PDFs fall back to
   docling (isolated subprocess — its native onnx can segfault the parent).
   Conversion never touches the brain DB (crash safety).
-- `index_mail` is a deprecation shim for `bin/brain/index.go --rebuild`. Ladybug
+- `index_mail` always rebuilds from scratch (repo corpus + mail). Ladybug
   corrupts its WAL when brand-new leafs are bulk-inserted while FTS/vector
   indexes exist; a fresh DB with indexes created last is the only safe path.
   Keep conversion + indexing separate so a conversion crash can't leave the
@@ -80,10 +76,6 @@ bin/facts/audit ["self"|"facts"|"info"|"stale"]   # 2-source + staleness gate
 bin/facts/crm [--dry-run]                         # proof person↔company/company↔project (ooCRM × corpus SoT)
 bin/kb/search "query" [--repo X]                  # deprecated wrapper → bin/brain/search.go
 bin/brain/search.go "query" [--root facts|info]   # deduction search → YAML
-bin/brain/get.go <id> [--body]
-bin/markdown/import.go [dir]                      # mistune leaves → YAML
-bin/git/import.go [REPO] [--json] [--limit N]     # go-git history → commit leafs
-bin/postgres/query.go --profile onlyoffice -c 'SELECT 1'
 bin/md/tables                                     # what the graph holds → YAML
 bin/brain/deduce "question"                       # thinking wrapper
 ```

PLAN.md

@@ -29,7 +29,7 @@ detective method: **a fact needs ≥2 independent sources or it is
 | D3 | web search | Vendored client; SearXNG URL is config. Optional Compose instance (sanitized settings). Do not run a second copy on a host that already has one. Empty/`throttled` ≠ “nothing exists”. |
 | D4 | embeddings | **model2vec** `minishlab/potion-multilingual-128M` instead of embeddinggemma. |
 | D5 | parser | **mistune** for MD → leaf extraction (duckdb-md documented as future optional SQL/export layer, not v1). |
-| D6 | graph engine | **LadybugDB**. Go is the service (`bin/brain/search.go`, `bin/brain/serve.go` in-process, `internal/brain`); Python remains for index/write until the Go write path is safe. |
+| D6 | graph engine | **LadybugDB**. Go is the service (`bin/brain/search.go`, `internal/brain`); Python remains for index/write until the Go write path is safe. |
 | D7 | db access | `db-yaml`/`psql-yq`-style, read-only, YAML out. OnlyOffice Postgres via SSH tunnel (`127.0.0.1:5433`). |
 | D8 | evidence | detective method: ≥2 independent sources or `(not confirmed)`. Auto-pair docker ps × compose × ssh-config × docs. |
 | D9 | facts/goal model | Who / What / How / Where / When + evidence + confidence on every edge. |
@@ -42,7 +42,6 @@ detective method: **a fact needs ≥2 independent sources or it is
 | D16 | contradictions | ≥2 yes vs ≥2 no → unrelated sources conflict → hypothesis → `(not confirmed)`. Resolution (authority, staleness adjudication) = **v2**, tracked as open question. |
 | D17 | assertion gate | Fact-check every *claim* (facts → info → live sources → web), not every edit. Missing graph ≠ “does not exist”. |
 | D18 | reasoner | Pluggable OpenAI-compatible URL. RAM: Qwen3.5-9B. Quality: Bonsai-27B or Qwen3.6-27B. No official Qwen3.6-9B. |
-| D19 | git history | [go-git](https://github.com/go-git/go-git) via `bin/git/import.go`. No subprocess of the git binary. Conversion prints commit leafs; brain write is `bin/brain/index.go`. |
 
 ## Architecture
 
@@ -50,22 +49,15 @@ detective method: **a fact needs ≥2 independent sources or it is
 2dph/
   PLAN.md / AGENTS.md
   docs/                     published docs (this conversation → docs/ as md)
-  skills/                   in-project skills (web-search, db-yaml, brain, diataxis-docs)
+  skills/                   in-project skills (web-search, db-yaml, kb-search, agent-cost, diataxis-docs, …)
   bin/
     facts/extract           auto-pair 2 sources → lexicon yaml + graph
     facts/audit             ["self"|"facts"|"info"|"stale"] 2-source + staleness gate
-    kb/index                Python write path (called by bin/brain/index.go)
-    brain/index.go          rebuild FTS + HNSW (incl. --with-mail)
-    brain/get.go stats.go eval.go watch.go
+    kb/index                build FTS + HNSW from corpus (Python, for now)
     brain/search.go         deduction: facts → info → web-search
-    brain/serve.go          HTTP API in-process (internal/httpapi + internal/brain)
-    mail/import.go          JSON → markdown (no brain write)
-    markdown/import.go      mistune leaves
-    postgres/query.go       read-only YAML (wraps bin/db/psql-yq)
-    git/import.go           go-git history (no git binary; conversion only)
-    chats/sync.go import.go facts.go apply.go
-                            (libs in internal/chats; no chats index)
-    md/import               (deprecated; bin/markdown/import.go)
+    kb/get  kb/stats  kb/eval
+    brain/serve.go          HTTP API (internal/httpapi)
+    md/import  md/select  md/tables  md/gaps     (mistune)
     brain/extract  brain/audit   brain/deduce    (thinking wrapper)
     web/search               (vendored)
     db/psql-yq               (vendored)
@@ -114,13 +106,12 @@ Common props on every node/edge: `root`, `confidence`, `evidence[]`, `how`,
 
 1. `bin/mail/sync.go` (Go, 8 workers) — paginated Gmail/OnlyOffice download.
    Gmail attachments key off `body.attachmentId`, not MIME `partId`.
-2. `bin/mail/import.go --from-raw` — message.json → message.md; PDFs via
+2. `bin/mail/import --from-raw` — message.json → message.md; PDFs via
    `pdftotext -layout` (~15ms) with docling subprocess fallback; ICS sidecars
    Latin-1→UTF-8 normalized.
-3. `bin/brain/index.go --rebuild` — fresh rebuild (repo corpus + mail) because ladybug
+3. `bin/mail/index_mail` — fresh rebuild (repo corpus + mail) because ladybug
    corrupts its WAL on bulk-insert into an already-indexed DB. Conversion and
-   indexing stay separate for crash safety. `bin/mail/index_mail` is a
-   deprecation shim.
+   indexing stay separate for crash safety.
 4. Result: 17,835 messages → 28,918 info leafs, FTS + HNSW healthy, searchable
    via `bin/brain/search.go`.
 
@@ -132,7 +123,7 @@ Common props on every node/edge: `root`, `confidence`, `evidence[]`, `how`,
 2. `go test ./internal/brain/rank` (cgo-free ranking + flag parser)
 3. python -m unittest discover -s bin/tools (includes published-docs SoT)
 4. bin/facts/audit self  (lexicon internal consistency)
-5. bin/brain/eval.go       (recall@5 ≥ 0.95, gates index regressions)
+5. bin/kb/eval            (recall@5 ≥ 0.95, gates index regressions)
 6. md-docs build/lint if docs tooling arrives.
 
 Feedback loop: every commit → PR → CI → green/gate → merge. Same discipline as
@@ -142,7 +133,7 @@ Feedback loop: every commit → PR → CI → green/gate → merge. Same discipl
 
 1. scaffold repo (:done after this file + AGENTS.md + .gitignore + ci)
 2. gh repo create eSlider/2dph --private + initial commit + CI
-3. vendored skill integration (web-search, db-yaml, brain, diataxis-docs) — no remote links
+3. vendored skill integration (web-search, db-yaml, kb-search, agent-cost, diataxis-docs) — no remote links
 4. .venv: ladybug + model2vec + mistune
 5. schema + tools with TDD (kb + md + facts + brain)
 6. ~/.config/brain config

README.md

@@ -30,8 +30,8 @@ graph TB
     subgraph dph["2dph tools"]
         EX["bin/facts/extract<br/>2-source pairing"]
         AU["bin/facts/audit<br/>confidence + staleness"]
-        IDX["bin/brain/index.go<br/>chunk + embed"]
-        MD["bin/markdown/import.go<br/>mistune leaves"]
+        IDX["bin/kb/index<br/>chunk + embed"]
+        MD["bin/md/import<br/>mistune leaves"]
         SR["bin/brain/search.go<br/>deduction"]
     end
 
@@ -88,28 +88,19 @@ fact; conflicting sources or a single source → `hypothesis` → `(not confirme
 bin/brain/search.go "Matrix federation over HTTPS"   # facts → info → web-search
 bin/brain/search.go "onlyoffice postgres" --root facts
 bin/brain/search.go "where is cs-lexicon" --json | yq '.'
-bin/brain/get.go <id> --body                         # full chunk on demand
-bin/brain/stats.go                                   # index health
-bin/brain/eval.go                                    # recall@5 gate
+bin/kb/get <id> --body                               # full chunk on demand
+bin/kb/stats                                         # index health
+bin/kb/eval                                          # recall@5 gate
 ```
 
 `--hop` is not implemented (needs File/FROM_FILE edges); the flag errors instead of walking. `bin/kb/search` is a deprecated wrapper around `bin/brain/search.go`.
 
-Git history is read with [go-git](https://github.com/go-git/go-git) (no git binary):
-
-```bash
-bin/git/import.go --json --limit 100              # commit leafs for this repo
-bin/git/import.go --root "$PROJECTS_ROOT" --json  # one pass per .git under root
-```
-
-Conversion only. Graph write (`File-[:HAS_VERSION]->Commit-[:AUTHORED]->Person`) stays with `bin/brain/index.go`.
-
 Mail is a first-class corpus (retrievable through the same search):
 
 ```bash
 bin/mail/sync.go --source onlyoffice,gmail --workers 8 --out var/mail  # raw sync (Go)
-bin/mail/import.go --from-raw var/mail                                  # JSON → markdown
-bin/brain/index.go --rebuild                                            # rebuild brain (incl. mail)
+bin/mail/import --from-raw var/mail                                     # JSON → markdown
+bin/mail/index_mail                                                     # rebuild brain incl. mail
 bin/brain/search.go "invoice from last week"                            # same search over mail leafs
 ```
 
@@ -120,7 +111,7 @@ bin/brain/search.go "invoice from last week"                            # same s
   readers. **Never `DROP INDEX` FTS/VECTOR** on Ladybug 0.19: DROP leaves
   ghost catalog tables (`_0_Leaf_vec_UPPER`) so recreate fails while
   `SHOW_INDEXES` omits HNSW. Fresh indexes = delete `var/kb.lbug` +
-  `bin/brain/index.go --rebuild`. Use `ensure_indexes()` after upserts.
+  `bin/kb/index --rebuild`. Use `ensure_indexes()` after upserts.
 - **model2vec** — `potion-multilingual-128M` static embeddings (256-dim),
   CPU-fast, deterministic, no Ollama runtime dependency.
 - facts and info split semantically by `root` column but written inside the
@@ -130,8 +121,8 @@ bin/brain/search.go "invoice from last week"                            # same s
 
 `bin/{subject}/{method}.go` — self-describing: shebang on line 1, usage comment
 from line 2. Shared code in `internal/`. YAML default output, `--json` for
-machines. Tests gate every commit. HTTP: `bin/brain/serve.go` calls
-`internal/brain` in-process (`/health` `/search` `/get` `/stats` `/audit` `/ingest`).
+machines. Tests gate every commit. HTTP: `bin/brain/serve.go` (default search
+binary `var/bin/brain-search`, not Python).
 
 ## Development
 

bin/brain/doc.go

@@ -1,3 +1,3 @@
-// Commands in this directory are shebang mains (search.go, serve.go, index.go,
-// get.go, stats.go, eval.go, watch.go), each behind an exclusive build tag.
+// Commands in this directory are shebang mains (search.go).
+// search.go is behind the system_ladybug build tag (cgo).
 package main

bin/brain/eval.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=brain_eval "$0" "$@"; exit
-//go:build brain_eval
-//
-// bin/brain/eval.go - recall@5 gate.
-//
-//	./bin/brain/eval.go
-//	./bin/brain/eval.go --json
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/kb/eval", os.Args[1:]))
-}

bin/brain/get.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=brain_get "$0" "$@"; exit
-//go:build brain_get
-//
-// bin/brain/get.go - read one leaf by id.
-//
-//	./bin/brain/get.go <id>
-//	./bin/brain/get.go <id> --body
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/kb/get", os.Args[1:]))
-}

bin/brain/index.go

@@ -1,24 +0,0 @@
-//usr/bin/env go run -tags=brain_index "$0" "$@"; exit
-//go:build brain_index
-//
-// bin/brain/index.go - rebuild the Ladybug graph (Python write path).
-//
-//	./bin/brain/index.go --rebuild
-//	./bin/brain/index.go --rebuild --with-mail
-//	./bin/brain/index.go --dry-run --with-mail
-//
-// v1 write is always a rebuild when mail is included (live FTS/HNSW + bulk
-// insert corrupts Ladybug 0.19 WAL). `add` is v2.
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	args := append([]string{"--with-mail"}, os.Args[1:]...)
-	os.Exit(cmdbin.ExecFile("bin/kb/index", args))
-}

bin/brain/serve.go

@@ -1,20 +1,18 @@
-//usr/bin/env go run -tags=brain_serve,system_ladybug "$0" "$@"; exit
-//go:build brain_serve && cgo && system_ladybug
+//usr/bin/env go run -tags=brain_serve "$0" "$@"; exit
+//go:build brain_serve
 //
-// bin/brain/serve.go - HTTP API (in-process ladybug search).
+// bin/brain/serve.go - HTTP API for the 2dph brain.
 //
 //	KB_ROOT=/path/to/2dph ./bin/brain/serve.go
-//	KB_WORKERS=4 KB_PORT=8630 ./bin/brain/serve.go
+//	KB_SEARCH_CMD=... KB_WORKERS=4 KB_PORT=8630 ./bin/brain/serve.go
 //
-// Needs CGO + libladybug (same as bin/brain/search.go).
+// Default search backend is var/bin/brain-search (Go), not Python.
 // NOTE: never run `gofmt -w` on this file — it breaks the shebang.
 package main
 
 import (
-	"log"
 	"os"
 
-	"github.com/eSlider/2dph/internal/brain"
 	"github.com/eSlider/2dph/internal/httpapi"
 )
 
@@ -24,8 +22,5 @@ func main() {
 			os.Setenv("KB_ROOT", wd)
 		}
 	}
-	if err := brain.Ready(); err != nil {
-		log.Fatal(err)
-	}
-	httpapi.Run(brain.HTTP{})
+	httpapi.Run()
 }

bin/brain/serve_exec.go

@@ -1,20 +0,0 @@
-//go:build brain_serve && !system_ladybug
-//
-// Fallback serve when ladybug cgo is not in the build (CI / tags=brain_serve).
-// Production shebang is serve.go (in-process).
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/httpapi"
-)
-
-func main() {
-	if os.Getenv("KB_ROOT") == "" {
-		if wd, err := os.Getwd(); err == nil {
-			os.Setenv("KB_ROOT", wd)
-		}
-	}
-	httpapi.Run(nil)
-}

bin/brain/stats.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=brain_stats "$0" "$@"; exit
-//go:build brain_stats
-//
-// bin/brain/stats.go - index health.
-//
-//	./bin/brain/stats.go
-//	./bin/brain/stats.go --json
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/kb/stats", os.Args[1:]))
-}

bin/brain/watch.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=brain_watch "$0" "$@"; exit
-//go:build brain_watch
-//
-// bin/brain/watch.go - re-index when corpus files change.
-//
-//	./bin/brain/watch.go [dir...]
-//	KB_WATCH_INTERVAL=15 ./bin/brain/watch.go
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/bin/watch"
-)
-
-func main() {
-	watch.Run(os.Args[1:])
-}

bin/chats/apply.go

@@ -1,19 +0,0 @@
-//usr/bin/env go run -tags=chats_apply "$0" "$@"; exit
-//go:build chats_apply
-//
-// bin/chats/apply.go - push extracted chat facts to OnlyOffice CRM.
-//
-//	./bin/chats/apply.go [--dry-run]
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/chats"
-)
-
-func main() {
-	os.Exit(chats.RunApply(os.Args[1:]))
-}

bin/chats/apply_cmd.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"bytes"
@@ -24,7 +24,7 @@ type ooContact struct {
 	} `json:"commonData"`
 }
 
-func RunApply(args []string) int {
+func runApply(args []string) int {
 	fs := flag.NewFlagSet("chats apply", flag.ContinueOnError)
 	dryRun := fs.Bool("dry-run", false, "show what would be done without writing")
 	help := fs.Bool("help", false, "")
@@ -176,7 +176,7 @@ func RunApply(args []string) int {
 }
 
 func loadFacts() ([]ExtractedFact, error) {
-	factsPath := filepath.Join(Dir(), "facts", "chat-facts.json")
+	factsPath := filepath.Join(chatsDir(), "facts", "chat-facts.json")
 	data, err := os.ReadFile(factsPath)
 	if err != nil {
 		if os.IsNotExist(err) {

bin/chats/chats_test.go

@@ -3,7 +3,7 @@
 // These are integration tests using real data and real Telegram API (when
 // credentials are available). They follow the TDD workflow pattern:
 // sync → import → facts → verify.
-package chats
+package main
 
 import (
 	"encoding/json"
@@ -48,7 +48,7 @@ func TestChatsImport(t *testing.T) {
 	t.Cleanup(func() { os.Chdir(cwd) })
 	t.Setenv("KB_ROOT", dir)
 
-	exitCode := RunImport([]string{})
+	exitCode := runImport([]string{})
 	if exitCode != 0 {
 		t.Fatalf("import exit code %d", exitCode)
 	}
@@ -140,7 +140,7 @@ func TestChatsImportEmpty(t *testing.T) {
 	t.Cleanup(func() { os.Chdir(cwd) })
 	t.Setenv("KB_ROOT", dir)
 
-	exitCode := RunImport([]string{})
+	exitCode := runImport([]string{})
 	if exitCode == 0 {
 		t.Fatal("expected non-zero exit for empty data dir")
 	}
@@ -171,7 +171,7 @@ func TestChatsRoundTrip(t *testing.T) {
 	t.Cleanup(func() { os.Chdir(cwd) })
 	t.Setenv("KB_ROOT", dir)
 
-	if code := RunImport([]string{}); code != 0 {
+	if code := runImport([]string{}); code != 0 {
 		t.Fatalf("import exit %d", code)
 	}
 

bin/chats/doc.go

@@ -1,4 +0,0 @@
-// Commands in this directory are shebang mains (sync.go, import.go, facts.go,
-// apply.go), each behind an exclusive build tag so `go build ./bin/chats`
-// does not see two mains. Shared code lives in internal/chats.
-package main

bin/chats/facts.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=chats_facts "$0" "$@"; exit
-//go:build chats_facts
-//
-// bin/chats/facts.go - extract phone/email/linkedin facts from JSONL.
-//
-//	./bin/chats/facts.go
-//
-// Writes var/chats/facts/. Does not index the brain.
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/chats"
-)
-
-func main() {
-	os.Exit(chats.RunFacts(os.Args[1:]))
-}

bin/chats/facts_cmd.go

@@ -1,11 +1,13 @@
-package chats
+package main
 
 import (
 	"bufio"
+	"bytes"
 	"encoding/json"
 	"flag"
 	"fmt"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"regexp"
 	"strings"
@@ -75,7 +77,7 @@ type ExtractedFact struct {
 	MessageID string `json:"message_id"`
 }
 
-func RunFacts(args []string) int {
+func runFacts(args []string) int {
 	fs := flag.NewFlagSet("chats facts", flag.ContinueOnError)
 	help := fs.Bool("help", false, "")
 	fs.SetOutput(os.Stderr)
@@ -87,7 +89,7 @@ func RunFacts(args []string) int {
 		return 0
 	}
 
-	root := Dir()
+	root := chatsDir()
 	telegramDir := filepath.Join(root, "telegram")
 
 	entries, err := os.ReadDir(telegramDir)
@@ -147,7 +149,7 @@ func RunFacts(args []string) int {
 	}
 	fmt.Printf("chats facts: saved to %s\n", factsPath)
 
-	writeFactsMarkdown(allFacts)
+	writeFactsToBrain(root, allFacts)
 
 	return 0
 }
@@ -271,10 +273,14 @@ func filterFacts(facts []ExtractedFact, factType string) []ExtractedFact {
 	return result
 }
 
-// writeFactsMarkdown stores a sidecar for humans. Brain ingest is
-// bin/brain/index.go (not this subject).
-func writeFactsMarkdown(facts []ExtractedFact) {
-	mdDir := filepath.Join(Dir(), "facts")
+func writeFactsToBrain(root string, facts []ExtractedFact) {
+	indexScript := filepath.Join(root, "bin", "kb", "index")
+	if _, err := os.Stat(indexScript); os.IsNotExist(err) {
+		fmt.Fprintf(os.Stderr, "chats facts: kb/index not found, skipping brain write\n")
+		return
+	}
+
+	mdDir := filepath.Join(chatsDir(), "facts")
 	if err := os.MkdirAll(mdDir, 0755); err != nil {
 		fmt.Fprintf(os.Stderr, "chats facts: mkdir %s: %v\n", mdDir, err)
 		return
@@ -282,7 +288,7 @@ func writeFactsMarkdown(facts []ExtractedFact) {
 
 	var sb strings.Builder
 	sb.WriteString("---\n")
-	sb.WriteString("root: info\n")
+	sb.WriteString("root: facts\n")
 	sb.WriteString("---\n\n")
 	sb.WriteString("# Chat-Derived Facts\n\n")
 	for _, f := range facts {
@@ -296,5 +302,15 @@ func writeFactsMarkdown(facts []ExtractedFact) {
 		fmt.Fprintf(os.Stderr, "chats facts: write %s: %v\n", factsMD, err)
 		return
 	}
-	fmt.Printf("chats facts: markdown %s (index via brain, not chats)\n", factsMD)
+
+	cmd := exec.Command(indexScript, "--corpus", mdDir, "--skip-indexes")
+	var outBuf, errBuf bytes.Buffer
+	cmd.Stdout = &outBuf
+	cmd.Stderr = &errBuf
+	cmd.Dir = root
+	if err := cmd.Run(); err != nil {
+		fmt.Fprintf(os.Stderr, "chats facts: brain index: %v\n%s", err, errBuf.String())
+		return
+	}
+	fmt.Printf("chats facts: written to brain (%s)\n", strings.TrimSpace(outBuf.String()))
 }

bin/chats/import.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=chats_import "$0" "$@"; exit
-//go:build chats_import
-//
-// bin/chats/import.go - JSONL → markdown under var/chats/md/.
-//
-//	./bin/chats/import.go
-//
-// Conversion only. Brain ingest is bin/brain/index.go, not this command.
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/chats"
-)
-
-func main() {
-	os.Exit(chats.RunImport(os.Args[1:]))
-}

bin/chats/import_cmd.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"bufio"
@@ -13,7 +13,7 @@ import (
 	"strings"
 )
 
-func RunImport(args []string) int {
+func runImport(args []string) int {
 	fs := flag.NewFlagSet("chats import", flag.ContinueOnError)
 	help := fs.Bool("help", false, "")
 	fs.SetOutput(os.Stderr)
@@ -25,7 +25,7 @@ func RunImport(args []string) int {
 		return 0
 	}
 
-	root := Dir()
+	root := chatsDir()
 	mdRoot := filepath.Join(root, "md")
 	glob := filepath.Join(root, "telegram", "*", "messages.jsonl")
 

bin/chats/index_cmd.go

@@ -0,0 +1,56 @@
+package main
+
+import (
+	"bytes"
+	"flag"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+)
+
+func runIndex(args []string) int {
+	fs := flag.NewFlagSet("chats index", flag.ContinueOnError)
+	help := fs.Bool("help", false, "")
+	fs.SetOutput(os.Stderr)
+	if err := fs.Parse(args); err != nil {
+		return 2
+	}
+	if *help {
+		fmt.Fprintln(os.Stderr, "usage: chats index")
+		return 0
+	}
+
+	root := repoRoot()
+	mdDir := filepath.Join(chatsDir(), "md")
+
+	_, err := os.Stat(mdDir)
+	if os.IsNotExist(err) {
+		fmt.Fprintf(os.Stderr, "chats index: no chat markdown at %s; run 'chats import' first\n", mdDir)
+		return 1
+	}
+
+	indexScript := filepath.Join(root, "bin", "kb", "index")
+	if _, err := os.Stat(indexScript); os.IsNotExist(err) {
+		fmt.Fprintf(os.Stderr, "chats index: %s not found\n", indexScript)
+		return 1
+	}
+
+	cmd := exec.Command(indexScript, "--corpus", mdDir)
+	var outBuf, errBuf bytes.Buffer
+	cmd.Stdout = &outBuf
+	cmd.Stderr = &errBuf
+	cmd.Dir = root
+
+	if err := cmd.Run(); err != nil {
+		fmt.Fprintf(os.Stderr, "chats index: %v\n%s", err, errBuf.String())
+		return 1
+	}
+	result := strings.TrimSpace(outBuf.String())
+	if result == "" {
+		result = strings.TrimSpace(errBuf.String())
+	}
+	fmt.Printf("chats index: %s\n", result)
+	return 0
+}

bin/chats/linkedin.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"bufio"

bin/chats/linkedin_test.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"errors"

bin/chats/main.go

@@ -0,0 +1,115 @@
+// bin/chats - sync, import, index, extract facts, and apply chat data
+// from Telegram, WhatsApp, LinkedIn into the brain and OnlyOffice CRM.
+//
+// Usage:
+//
+//	chats sync telegram   [--limit N] [--since DATE] [--phone PHONE]
+//	chats sync whatsapp   [--qr] [--limit N]
+//	chats sync linkedin   [--limit N]
+//	chats import                           # JSONL → MD (all sources)
+//	chats index                            # rebuild var/kb.lbug with chats
+//	chats facts                            # extract + cross-check
+//	chats apply          [--dry-run]       # push to OnlyOffice CRM
+package main
+
+import (
+	"fmt"
+	"os"
+	"strings"
+)
+
+func main() {
+	if len(os.Args) < 2 {
+		usage()
+		os.Exit(2)
+	}
+	cmd := os.Args[1]
+	args := os.Args[2:]
+	switch cmd {
+	case "sync":
+		if len(args) < 1 {
+			usage()
+			os.Exit(2)
+		}
+		platform := args[0]
+		platformArgs := args[1:]
+		switch platform {
+		case "telegram":
+			os.Exit(runSyncTelegram(platformArgs))
+		case "whatsapp":
+			fmt.Fprintf(os.Stderr, "chats: WhatsApp not implemented yet\n")
+			os.Exit(1)
+		case "linkedin":
+			os.Exit(runSyncLinkedIn(platformArgs))
+		default:
+			fmt.Fprintf(os.Stderr, "chats: unknown platform %q\n", platform)
+			os.Exit(2)
+		}
+	case "import":
+		os.Exit(runImport(args))
+	case "index":
+		os.Exit(runIndex(args))
+	case "facts":
+		os.Exit(runFacts(args))
+	case "apply":
+		os.Exit(runApply(args))
+	case "help", "-h", "--help":
+		usage()
+		return
+	default:
+		fmt.Fprintf(os.Stderr, "chats: unknown command %q\n", cmd)
+		usage()
+		os.Exit(2)
+	}
+}
+
+func usage() {
+	w := os.Stderr
+	fmt.Fprintln(w, `Usage: chats <command> [args]
+
+Commands:
+  sync telegram  [--limit N] [--since DATE] [--phone PHONE]
+  sync whatsapp  [--qr] [--limit N]
+  sync linkedin  [--limit N]
+  import                             JSONL → MD (all sources)
+  index                              rebuild var/kb.lbug with chats
+  facts                              extract + cross-check facts
+  apply             [--dry-run]      push to OnlyOffice CRM
+
+Output layout:
+  var/chats/<platform>/<chat_id>/messages.jsonl
+  var/chats/md/<platform>/<chat_name>/messages.md`)
+}
+
+// repoRoot locates the 2dph project root by walking up from the binary.
+func repoRoot() string {
+	if v := os.Getenv("KB_ROOT"); v != "" {
+		return v
+	}
+	wd, err := os.Getwd()
+	if err != nil {
+		return "."
+	}
+	for i := 0; i < 10; i++ {
+		if _, err := os.Stat(wd + "/var"); err == nil {
+			return wd
+		}
+		if _, err := os.Stat(wd + "/.git"); err == nil {
+			return wd
+		}
+		parent := wd
+		if idx := strings.LastIndex(wd, "/"); idx >= 0 {
+			parent = wd[:idx]
+		}
+		if parent == wd {
+			break
+		}
+		wd = parent
+	}
+	return "."
+}
+
+// chatsDir returns var/chats under the repo root.
+func chatsDir() string {
+	return repoRoot() + "/var/chats"
+}

bin/chats/mcpclient.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"bufio"

bin/chats/source.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"context"

bin/chats/sync.go

@@ -1,41 +0,0 @@
-//usr/bin/env go run -tags=chats_sync "$0" "$@"; exit
-//go:build chats_sync
-//
-// bin/chats/sync.go - download chat messages to var/chats/<platform>/.
-//
-//	./bin/chats/sync.go telegram [--limit N] [--phone PHONE]
-//	./bin/chats/sync.go linkedin [--limit N] [--refresh]
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"fmt"
-	"os"
-
-	"github.com/eSlider/2dph/internal/chats"
-)
-
-func main() {
-	if len(os.Args) < 2 {
-		fmt.Fprintln(os.Stderr, `usage: bin/chats/sync.go telegram|linkedin [flags]`)
-		os.Exit(2)
-	}
-	platform := os.Args[1]
-	args := os.Args[2:]
-	switch platform {
-	case "telegram":
-		os.Exit(chats.RunSyncTelegram(args))
-	case "linkedin":
-		os.Exit(chats.RunSyncLinkedIn(args))
-	case "whatsapp":
-		fmt.Fprintln(os.Stderr, "chats: WhatsApp not implemented yet")
-		os.Exit(1)
-	case "help", "-h", "--help":
-		fmt.Fprintln(os.Stderr, `usage: bin/chats/sync.go telegram|linkedin [flags]`)
-		return
-	default:
-		fmt.Fprintf(os.Stderr, "chats: unknown platform %q\n", platform)
-		os.Exit(2)
-	}
-}

bin/chats/sync_cmd.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"context"
@@ -11,7 +11,7 @@ import (
 	"time"
 )
 
-func RunSyncTelegram(args []string) int {
+func runSyncTelegram(args []string) int {
 	fs := flag.NewFlagSet("chats sync telegram", flag.ContinueOnError)
 	limit := fs.Int("limit", 0, "max messages per chat (0 = all)")
 	phone := fs.String("phone", "", "phone number (default env TELEGRAM_PHONE)")
@@ -78,7 +78,7 @@ func RunSyncTelegram(args []string) int {
 	defer cancel()
 
 	start := time.Now()
-	if err := src.Sync(ctx, Dir(), *limit); err != nil {
+	if err := src.Sync(ctx, chatsDir(), *limit); err != nil {
 		fmt.Fprintf(os.Stderr, "chats sync telegram: %v\n", err)
 		return 1
 	}

bin/chats/sync_linkedin_cmd.go

@@ -1,4 +1,4 @@
-package chats
+package main
 
 import (
 	"context"
@@ -28,7 +28,7 @@ func checkLinkedInSession(userDataDir string) (bool, error) {
 	return false, nil
 }
 
-func RunSyncLinkedIn(args []string) int {
+func runSyncLinkedIn(args []string) int {
 	fs := flag.NewFlagSet("chats sync linkedin", flag.ContinueOnError)
 	limit := fs.Int("limit", 0, "max messages per conversation (0 = all)")
 	refresh := fs.Bool("refresh", false, "refresh session from live webtop browser before sync")
@@ -72,7 +72,7 @@ func RunSyncLinkedIn(args []string) int {
 	defer cancel()
 
 	start := time.Now()
-	if err := src.Sync(ctx, Dir(), *limit); err != nil {
+	if err := src.Sync(ctx, chatsDir(), *limit); err != nil {
 		fmt.Fprintf(os.Stderr, "chats sync linkedin: %v\n", err)
 		return 1
 	}

bin/docker-entrypoint

@@ -2,10 +2,10 @@
 # bin/docker-entrypoint - run 2dph tools inside the container.
 #
 #   brain                 shell (default)
-#   brain search <q>      bin/brain/search.go
-#   brain index           bin/kb/index --with-mail
-#   brain watch <dir>     compiled /app/bin/watch (bin/brain/watch.go)
-#   brain serve           compiled /app/bin/serve (bin/brain/serve.go)
+#   brain search <q>      bin/kb/search
+#   brain index           bin/kb/index
+#   brain watch <dir>     watchdog re-indexer (bin/kb/watch)
+#   brain serve           async Go HTTP server (bin/serve)
 #   brain extract         bin/facts/extract (docker×compose pairing)
 #   brain audit           bin/facts/audit
 #
@@ -18,7 +18,7 @@ shift || true
 case "$CMD" in
   shell) exec bash ;;
   search) exec "$KB_PY" /app/bin/kb/search "$@" ;;
-  index) exec "$KB_PY" /app/bin/kb/index --with-mail "$@" ;;
+  index) exec "$KB_PY" /app/bin/kb/index "$@" ;;
   watch) exec /app/bin/watch "$@" ;;
   serve) exec /app/bin/serve "$@" ;;
   extract) exec "$KB_PY" /app/bin/facts/extract "$@" ;;

bin/git/import

@@ -1,25 +1,153 @@
 #!/usr/bin/env python3
-"""git/import — deprecated. Use bin/git/import.go (go-git, no git binary).
+"""git/import - import git history (commits, authors, files) into the brain.
 
-  bin/git/import.go [REPO] [--json] [--limit N] [--since DATE]
+  bin/git/import [REPO]                 import all commits -> leafs + graph
+  bin/git/import --json                 emit import leafs as JSON, no write
+  bin/git/import --limit 100            cap commits processed
+  bin/git/import --since 2026-01-01     only recent commits
+  bin/git/import --root DIR             run per repo dir under DIR
+  bin/git/import --no-env               never read .env anywhere (default: true)
+
+Reads `git log --no-merges --name-only` from the repo, maps commits to
+`info` leafs (root=info, type=commit) and writes the version graph
+`File -[:HAS_VERSION]-> Commit -[:AUTHORED]-> Person` into var/kb.lbug.
+Idempotent: leaf MERGE by (source,text via leaf_id), graph MERGE by sha.
 """
 from __future__ import annotations
 
-import os
+import json
+import subprocess
 import sys
 from pathlib import Path
 
 ROOT = Path(__file__).resolve().parents[2]
+sys.path.insert(0, str(ROOT / "bin" / "tools"))
+
+from kblib import (  # noqa: E402
+    connect, ensure_indexes, init_schema, upsert_leaf,
+)
+from gitimport import commits_to_leafs, ensure_git_schema, index_commits, parse_log  # noqa: E402
+
+LOG_FMT = "--format=%x1e%H%x1f%an%x1f%ae%x1f%aI%x1f%s"
+
+
+def git_log(repo: Path, limit: int = 0, since: str = "") -> str:
+    cmd = ["git", "-C", str(repo), "log", "--no-merges", "--name-only", LOG_FMT]
+    if since:
+        cmd += ["--since", since]
+    if limit:
+        cmd += ["-n", str(limit)]
+    try:
+        out = subprocess.run(cmd, capture_output=True, text=True, timeout=120)
+    except (FileNotFoundError, subprocess.TimeoutExpired):
+        return ""
+    if out.returncode != 0:
+        print(f"git/import: {repo}: {out.stderr.strip()}", file=sys.stderr)
+        return ""
+    return out.stdout
+
+
+def repo_name(repo: Path) -> str:
+    try:
+        out = subprocess.run(
+            ["git", "-C", str(repo), "remote", "get-url", "origin"],
+            capture_output=True, text=True, timeout=20)
+        url = out.stdout.strip()
+        return url.rstrip("/").split("/")[-1].removesuffix(".git") if url else repo.name
+    except (FileNotFoundError, subprocess.TimeoutExpired):
+        return repo.name
+
+
+def embedder():
+    from model2vec import StaticModel
+    model = StaticModel.from_pretrained("minishlab/potion-multilingual-128M")
+    return lambda text: model.encode([text])[0].astype(float).tolist()
+
+
+def import_repo(conn, repo: Path, embed, limit: int, since: str,
+                no_write: bool = False) -> tuple[int, int]:
+    raw = git_log(repo, limit, since)
+    commits = parse_log(raw)
+    leafs = commits_to_leafs(commits, repo_name(repo))
+    if no_write:
+        return len(commits), 0
+    written = 0
+    for lf in leafs:
+        query = f"{lf['heading']}\n\n{lf['text']}"
+        emb = embed(lf["text"]) if lf["text"] else None
+        upsert_leaf(conn, text=query, root="info", confidence="confirmed",
+                    source=lf["source"], source_rev="git", how="git/import",
+                    loc=lf["source"], type_=lf.get("type", "commit"),
+                    embedding=emb)
+        written += 1
+    index_commits(conn, commits, repo_name(repo))
+    return len(commits), written
 
 
 def main(argv: list[str]) -> int:
-    print(
-        "bin/git/import is deprecated; use bin/git/import.go (go-git)",
-        file=sys.stderr,
-    )
-    target = ROOT / "bin" / "git" / "import.go"
-    os.execvp("go", ["go", "run", str(target), *argv])
-    return 1
+    import argparse
+    p = argparse.ArgumentParser(description="import git history into the brain")
+    p.add_argument("repo", nargs="?", default=None)
+    p.add_argument("--root", default=None, help="directory of repos to import (each git dir separately)")
+    p.add_argument("--limit", type=int, default=0)
+    p.add_argument("--since", default="")
+    p.add_argument("--json", action="store_true")
+    p.add_argument("--dry-run", action="store_true", help="parse + report, no db write")
+    a = p.parse_args(argv)
+
+    repos: list[Path] = []
+    if a.repo:
+        repos = [Path(a.repo)]
+    elif a.root:
+        root = Path(a.root)
+        if root.is_file():
+            repos = [root]
+        else:
+            repos = [dp for dp in sorted(root.iterdir()) if (dp / ".git").exists() or dp.is_file()]
+    else:
+        repos = [ROOT]
+
+    total_commits = 0
+    results: list[dict] = []
+    if a.dry_run:
+        for repo in repos:
+            if not repo.exists():
+                continue
+            commits = parse_log(git_log(repo, a.limit, a.since))
+            name = repo_name(repo)
+            total_commits += len(commits)
+            results.append({"repo": name, "commits": len(commits),
+                            "leafs": len(commits_to_leafs(commits, name)), "path": str(repo)})
+        if a.json:
+            print(json.dumps(results, indent=2))
+        else:
+            for r in results:
+                print(f"{r['repo']:<24} {r['commits']:>5} commits -> {r['leafs']} leafs  {r['path']}")
+        return 0
+
+    # Never DROP FTS/VECTOR (ghost catalog). Upsert while indexes exist is OK;
+    # ensure_indexes only CREATEs when missing.
+    db, conn = connect(ROOT / "var" / "kb.lbug", read_only=False)
+    init_schema(conn)
+    embed = embedder()
+    rows: list[dict] = []
+    for repo in repos:
+        if not repo.exists():
+            continue
+        reached, written = import_repo(conn, repo, embed, a.limit, a.since)
+        total_commits += reached
+        rows.append({"repo": repo_name(repo), "commits": reached, "written": written})
+    ensure_indexes(conn)
+    conn.close()
+    db.close()
+
+    if a.json:
+        print(json.dumps(rows, indent=2))
+    else:
+        for r in rows:
+            print(f"imported {r['commits']:>5} commits -> {r['written']} leafs  {r['repo']}")
+        print(f"total: {total_commits} commits")
+    return 0
 
 
 if __name__ == "__main__":

bin/git/import.go

@@ -1,143 +0,0 @@
-//usr/bin/env go run "$0" "$@"; exit
-//
-// bin/git/import.go - read git history with go-git (no git binary).
-//
-//	./bin/git/import.go [REPO]
-//	./bin/git/import.go --json
-//	./bin/git/import.go --limit 100 --since 2026-01-01
-//	./bin/git/import.go --root DIR
-//
-// Conversion only: prints commit leafs. Brain write is bin/brain/index.go.
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"encoding/json"
-	"fmt"
-	"os"
-	"path/filepath"
-	"strconv"
-	"time"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-	"github.com/eSlider/2dph/internal/gitlog"
-)
-
-func main() {
-	os.Exit(run(os.Args[1:]))
-}
-
-func run(args []string) int {
-	var repo, root, since string
-	limit := 0
-	jsonOut := false
-	i := 0
-	for i < len(args) {
-		a := args[i]
-		switch {
-		case a == "--json":
-			jsonOut = true
-		case a == "--limit" && i+1 < len(args):
-			i++
-			n, err := strconv.Atoi(args[i])
-			if err != nil || n < 0 {
-				fmt.Fprintf(os.Stderr, "git/import: --limit must be a non-negative integer\n")
-				return 2
-			}
-			limit = n
-		case a == "--since" && i+1 < len(args):
-			i++
-			since = args[i]
-		case a == "--root" && i+1 < len(args):
-			i++
-			root = args[i]
-		case a == "-h" || a == "--help":
-			fmt.Fprintln(os.Stderr, `usage: bin/git/import.go [REPO] [--json] [--limit N] [--since DATE] [--root DIR]`)
-			return 0
-		case len(a) > 0 && a[0] != '-':
-			repo = a
-		default:
-			fmt.Fprintf(os.Stderr, "git/import: unknown flag %s\n", a)
-			return 2
-		}
-		i++
-	}
-
-	var sinceT time.Time
-	if since != "" {
-		var err error
-		sinceT, err = parseSince(since)
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "git/import: %v\n", err)
-			return 2
-		}
-	}
-
-	repos := []string{}
-	if repo != "" {
-		repos = []string{repo}
-	} else if root != "" {
-		entries, err := os.ReadDir(root)
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "git/import: %v\n", err)
-			return 1
-		}
-		for _, e := range entries {
-			p := filepath.Join(root, e.Name())
-			if _, err := os.Stat(filepath.Join(p, ".git")); err == nil {
-				repos = append(repos, p)
-			}
-		}
-	} else {
-		repos = []string{cmdbin.Root()}
-	}
-
-	opt := gitlog.Options{Limit: limit, Since: sinceT}
-	type row struct {
-		Repo    string         `json:"repo"`
-		Path    string         `json:"path"`
-		Commits int            `json:"commits"`
-		Leafs   []gitlog.Leaf  `json:"leafs,omitempty"`
-	}
-	var rows []row
-	for _, p := range repos {
-		name, err := gitlog.RepoName(p)
-		if err != nil && name == "" {
-			fmt.Fprintf(os.Stderr, "git/import: %s: %v\n", p, err)
-			continue
-		}
-		cs, err := gitlog.Log(p, opt)
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "git/import: %s: %v\n", p, err)
-			return 1
-		}
-		leafs := make([]gitlog.Leaf, 0, len(cs))
-		for _, c := range cs {
-			leafs = append(leafs, gitlog.ToLeaf(c, name))
-		}
-		rows = append(rows, row{Repo: name, Path: p, Commits: len(cs), Leafs: leafs})
-	}
-
-	if jsonOut {
-		enc := json.NewEncoder(os.Stdout)
-		enc.SetIndent("", "  ")
-		enc.SetEscapeHTML(false)
-		if err := enc.Encode(rows); err != nil {
-			return 1
-		}
-		return 0
-	}
-	for _, r := range rows {
-		fmt.Printf("%-24s %5d commits  %s\n", r.Repo, r.Commits, r.Path)
-	}
-	return 0
-}
-
-func parseSince(s string) (time.Time, error) {
-	for _, layout := range []string{time.RFC3339, "2006-01-02"} {
-		if t, err := time.Parse(layout, s); err == nil {
-			return t, nil
-		}
-	}
-	return time.Time{}, fmt.Errorf("cannot parse --since %q", s)
-}

bin/kb/index

@@ -26,7 +26,6 @@ from kblib import (  # noqa: E402
     open_readonly, stats,
 )
 from mdleaves import read_markdown, to_all, walk_markdown  # noqa: E402
-from mailleafs import from_mail_root  # noqa: E402
 
 CORPUS_DEFAULTS = ["README.md", "PLAN.md", "AGENTS.md", "docs", "skills"]
 
@@ -100,9 +99,6 @@ def main(argv: list[str]) -> int:
     p = argparse.ArgumentParser(description="build the 2dph brain index")
     p.add_argument("--corpus", action="append", help="extra markdown dir/file to index (may repeat)")
     p.add_argument("--rebuild", action="store_true", help="fresh db + indexes")
-    p.add_argument("--with-mail", action="store_true", help="include var/mail message.md leafs")
-    p.add_argument("--since", default="", help="with --with-mail, only messages dated >= YYYY-MM-DD")
-    p.add_argument("--dry-run", action="store_true", help="count leafs, write nothing")
     p.add_argument(
         "--skip-indexes",
         action="store_true",
@@ -113,26 +109,14 @@ def main(argv: list[str]) -> int:
     a = p.parse_args(argv)
 
     from kblib import DB_PATH, VAR
+    VAR.mkdir(exist_ok=True)
+    if a.rebuild and DB_PATH.exists():
+        DB_PATH.unlink()
 
     leafs = load_corpus(ROOT)
     if a.corpus:
         for source in a.corpus:
             leafs.extend(load_corpus_glob(source))
-    mail_n = 0
-    if a.with_mail:
-        mail = from_mail_root(ROOT / "var" / "mail", since=a.since)
-        mail_n = len(mail)
-        leafs.extend(mail)
-
-    if a.dry_run:
-        msg = {"indexed": 0, "corpus_total": len(leafs), "mail_leafs": mail_n, "dry_run": True}
-        print(json.dumps(msg, indent=2) if a.json else
-              f"brain/index: {len(leafs)} leafs would be indexed (mail={mail_n})")
-        return 0
-
-    VAR.mkdir(exist_ok=True)
-    if a.rebuild and DB_PATH.exists():
-        DB_PATH.unlink()
 
     db, conn = connect(DB_PATH, read_only=False)
     init_schema(conn)

bin/kb/watch.go

@@ -1,5 +1,5 @@
 //usr/bin/env go run "$0" "$@"; exit
-// bin/kb/watch.go — deprecated. Use bin/brain/watch.go.
+// bin/kb/watch.go - re-index the 2dph brain when corpus files change.
 //
 // Usage:
 //

bin/mail/import

@@ -15,8 +15,8 @@ Writes one directory per message: var/mail/{folder}/{message_id}/
   attachments/              raw attachment files (zips unpacked to _unpacked/)
   attachments/*.md          converted attachment content
 
-Indexing is a separate step (`bin/brain/index.go --rebuild`): conversion can
-crash in native docling and must not leave the brain DB mid-transaction.
+Indexing is a separate step (bin/mail/index_mail): conversion can crash in
+native docling and must not leave the brain DB mid-transaction.
 
 Requires ONLYOFFICE_URL/USER/PASS in .env (or env). Idempotent: a message
 already present (message.md exists) is skipped unless --force.

bin/mail/import.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=mail_import "$0" "$@"; exit
-//go:build mail_import
-//
-// bin/mail/import.go - message.json → markdown (no brain write).
-//
-//	./bin/mail/import.go --from-raw var/mail
-//
-// Indexing is bin/brain/index.go --rebuild, not this command.
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/mail/import", os.Args[1:]))
-}

bin/mail/index_mail

@@ -1,26 +1,135 @@
 #!/usr/bin/env python3
-"""mail/index_mail — deprecated. Use bin/brain/index.go --rebuild --with-mail.
+"""mail/index_mail - rebuild the brain with every markdown under var/mail.
 
-Ladybug corrupts its WAL on bulk-insert into an already-indexed DB, so this
-shim always rebuilds (repo corpus + var/mail). Conversion stays in mail/import.
+Ladybug corrupts its WAL when brand-new leafs are bulk-inserted while the
+FTS/VECTOR indexes already exist, so indexing ALWAYS runs as a fresh rebuild
+(repo corpus + var/mail), matching the proven-safe `kb/index --rebuild` path.
+Conversion and indexing stay separate: conversion can crash in native docling
+and must not leave the brain DB mid-transaction.
+
+  bin/mail/index_mail                 rebuild the index incl. all mail
+  bin/mail/index_mail --dry-run       count without writing
+  bin/mail/index_mail --limit N       cap messages included
+  bin/mail/index_mail --since D       only messages dated >= D (YYYY-MM-DD)
 """
 from __future__ import annotations
 
-import os
+import argparse
+import json
 import sys
 from pathlib import Path
 
 ROOT = Path(__file__).resolve().parents[2]
+sys.path.insert(0, str(ROOT / "bin" / "tools"))
+
+from kblib import DB_PATH, VAR, connect, ensure_indexes, init_schema, stats, upsert_leaf  # noqa: E402
+from mdleaves import read_markdown, to_all, walk_markdown  # noqa: E402
+
+
+def msg_date(md: Path) -> str:
+    j = md.parent / "message.json"
+    try:
+        d = json.loads(j.read_text(encoding="utf-8"))
+        return (d.get("receivedDate") or d.get("receivedAt") or "")[:10]
+    except Exception:
+        return ""
+
+
+def mail_leafs(limit: int, since: str, repo: str = "ooMail") -> list[dict]:
+    root = ROOT / "var" / "mail"
+    mds = sorted(root.rglob("message.md"))
+    if since:
+        mds = [m for m in mds if msg_date(m) >= since]
+    if limit:
+        mds = mds[:limit]
+    leafs: list[dict] = []
+    for md in mds:
+        files = [md] + sorted((md.parent / "attachments").glob("*.md"))
+        for f in files:
+            if not f.exists():
+                continue
+            for lf in to_all(read_markdown(f), f, repo=repo):
+                lf["source"] = f"ooMail:{md.parent.name}:{f.name}"
+                lf["how"] = "mail/import"
+                leafs.append(lf)
+    return leafs
 
 
 def main(argv: list[str]) -> int:
-    print(
-        "bin/mail/index_mail is deprecated; use bin/brain/index.go --rebuild --with-mail",
-        file=sys.stderr,
-    )
-    index = ROOT / "bin" / "kb" / "index"
-    os.execv(sys.executable, [sys.executable, str(index), "--rebuild", "--with-mail", *argv])
-    return 1
+    p = argparse.ArgumentParser(description="rebuild the brain incl. all mail")
+    p.add_argument("--dry-run", action="store_true", help="count only, write nothing")
+    p.add_argument("--limit", type=int, default=0, help="cap messages included")
+    p.add_argument("--since", default="", help="only messages dated >= YYYY-MM-DD")
+    p.add_argument("--json", action="store_true")
+    a = p.parse_args(argv)
+
+    mail = mail_leafs(a.limit, a.since)
+    if a.dry_run:
+        print(f"mail/index_mail: {len(mail)} mail leafs would be indexed")
+        return 0
+
+    # Fresh rebuild: delete DB, index repo corpus + mail, create indexes once
+    # at the end. Never insert into an already-indexed DB (WAL corruption).
+    VAR.mkdir(exist_ok=True)
+    if DB_PATH.exists():
+        DB_PATH.unlink()
+
+    corpus = _load_corpus()
+    leafs = corpus + mail
+
+    db, conn = connect(DB_PATH, read_only=False)
+    init_schema(conn)
+    embed = _embedder()
+    done, total = _index_leafs(conn, leafs, embed)
+    ensure_indexes(conn)
+    s = stats(conn)
+    conn.close()
+    db.close()
+
+    result = {"indexed": done, "corpus_total": total, "mail_leafs": len(mail),
+              **{k: v for k, v in s.items() if k in ("total", "by_root")}}
+    print(json.dumps(result, indent=2) if a.json else
+          f"mail/index_mail: indexed {done}/{total} leafs (mail={len(mail)}); db total {s['total']}")
+    return 0
+
+
+CORPUS_DEFAULTS = ["README.md", "PLAN.md", "AGENTS.md", "docs", "skills"]
+
+
+def _load_corpus() -> list[dict]:
+    files: list[Path] = []
+    for entry in CORPUS_DEFAULTS:
+        p = ROOT / entry
+        if p.is_file():
+            files.append(p)
+        elif p.is_dir():
+            files.extend(walk_markdown(p))
+    leafs: list[dict] = []
+    for path in files:
+        try:
+            leafs.extend(to_all(read_markdown(path), path, repo="eSlider/2dph"))
+        except OSError as e:
+            print(f"mail/index_mail: skip {path}: {e}", file=sys.stderr)
+    return leafs
+
+
+def _index_leafs(conn, leafs: list[dict], embed_fn) -> tuple[int, int]:
+    count = 0
+    for lf in leafs:
+        query = f"{lf['heading']}\n\n{lf['text']}"
+        emb = embed_fn(lf["text"]) if lf["text"] else None
+        upsert_leaf(conn, text=query, root="info", confidence="confirmed",
+                    source=lf["source"], source_rev="mail" if lf.get("how") == "mail/import" else "working-tree",
+                    how=lf.get("how", "kb/index"), loc=lf["source"], type_=lf.get("type", "reference"),
+                    embedding=emb)
+        count += 1
+    return count, len(leafs)
+
+
+def _embedder():
+    from model2vec import StaticModel
+    model = StaticModel.from_pretrained("minishlab/potion-multilingual-128M")
+    return lambda text: model.encode([text])[0].astype(float).tolist()
 
 
 if __name__ == "__main__":

bin/mail/sync.go

@@ -6,7 +6,7 @@
 //	./bin/mail/sync.go --dry-run
 //
 // Writes raw message.json + attachments under var/mail/<folder>/<id>/; run
-// bin/mail/import.go --from-raw afterwards to convert everything to markdown.
+// bin/mail/import --from-raw afterwards to convert everything to markdown.
 //
 // Shebang trick: first line is a Go `//` comment; the real code lives in the
 // importable package (module path, never a relative import).

bin/markdown/doc.go

@@ -1,3 +0,0 @@
-// Commands in this directory are shebang mains (import.go), tagged so
-// `go build ./bin/markdown` does not see two mains.
-package main

bin/markdown/import.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=markdown_import "$0" "$@"; exit
-//go:build markdown_import
-//
-// bin/markdown/import.go - split markdown into leafs (mistune).
-//
-//	./bin/markdown/import.go [dir]
-//	./bin/markdown/import.go --files a.md,b.md --json
-//
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/md/import", os.Args[1:]))
-}

bin/postgres/doc.go

@@ -1,2 +0,0 @@
-// Commands in this directory are shebang mains (query.go).
-package main

bin/postgres/query.go

@@ -1,20 +0,0 @@
-//usr/bin/env go run -tags=postgres_query "$0" "$@"; exit
-//go:build postgres_query
-//
-// bin/postgres/query.go - read-only Postgres as YAML.
-//
-//	./bin/postgres/query.go --profile onlyoffice -c 'SELECT 1'
-//
-// Profiles: $HOME/.config/brain/db-profiles.yml (credentials stay out of git).
-// NOTE: never run `gofmt -w` on this file — it breaks the shebang.
-package main
-
-import (
-	"os"
-
-	"github.com/eSlider/2dph/internal/cmdbin"
-)
-
-func main() {
-	os.Exit(cmdbin.ExecFile("bin/db/psql-yq", os.Args[1:]))
-}

bin/serve.go

@@ -18,5 +18,5 @@ func main() {
 			os.Setenv("KB_ROOT", wd)
 		}
 	}
-	httpapi.Run(nil)
+	httpapi.Run()
 }

bin/tools/gitimport.py

@@ -1,12 +1,21 @@
-"""gitimport - Ladybug graph writes for Commit/File/Person (no git binary).
+"""gitimport - parse `git log` output and turn commits into brain leafs.
 
-Commit records come from bin/git/import.go (go-git). This module only MERGEs
-the version graph File-[:HAS_VERSION]->Commit-[:AUTHORED]->Person.
+Pure, testable functions. Field grammar (see bin/git/import):
+
+  git log --no-merges --name-only \
+      --format='%x1e%H%x1f%an%x1f%ae%x1f%aI%x1f%s'
+
+  0x1e = record separator, 0x1f = field separator.
+  Files: newline-separated lines following each record's subject.
 """
+
 from __future__ import annotations
 
 from dataclasses import dataclass, field
 
+REC_SEP = "\x1e"
+FIELD_SEP = "\x1f"
+
 
 @dataclass
 class Commit:
@@ -17,6 +26,54 @@ class Commit:
     subject: str
     files: list[str] = field(default_factory=list)
 
+    def leaf_text(self, repo: str) -> str:
+        head = f"commit {self.sha[:12]} in {repo} — {self.subject}"
+        body = [head, f"Author: {self.author} <{self.email}>", f"Date: {self.date}"]
+        if self.files:
+            body.append("Changing: " + ", ".join(self.files))
+        return "\n".join(body)
+
+
+def parse_log(text: str) -> list[Commit]:
+    """Parse `git log` output into Commit records.
+
+    Records are separated by 0x1e. A record is fields joined by 0x1f,
+    followed by optional newline-separated file paths inside the next
+    segment (git emits blank line + files after each record).
+    """
+    commits: list[Commit] = []
+    # field records and file lists alternate; simpler: split on REC_SEP,
+    # each chunk = header line, possibly followed by newline + files.
+    for chunk in text.split(REC_SEP):
+        chunk = chunk.strip("\n")
+        if not chunk:
+            continue
+        lines = chunk.split("\n", 1)
+        header = lines[0].split(FIELD_SEP)
+        if len(header) < 5:
+            continue
+        sha, author, email, date, subject = header[:5]
+        files = [ln.strip() for ln in lines[1].splitlines() if ln.strip()] if len(lines) > 1 else []
+        commits.append(Commit(sha=sha, author=author, email=email,
+                              date=date, subject=subject, files=files))
+    return commits
+
+
+def commits_to_leafs(commits: list[Commit], repo: str) -> list[dict]:
+    """Map commits to the leaf shape bin/kb/index expects (source/repo/...)."""
+    out: list[dict] = []
+    for c in commits:
+        out.append({
+            "source": f"{repo}@{c.sha}",
+            "repo": repo,
+            "heading": f"commit {c.sha[:12]} — {c.subject}",
+            "text": c.leaf_text(repo),
+            "type": "commit",
+            "status": "current",
+            "related": ",".join(c.files),
+        })
+    return out
+
 
 GIT_SCHEMA = (
     "CREATE NODE TABLE IF NOT EXISTS Commit (id STRING, repo STRING, subject STRING, "

bin/tools/kblib.py

@@ -135,7 +135,7 @@ def create_fts_and_vector(conn: ladybug.Connection, force: bool = False) -> None
 
     `force=True` is accepted for API compatibility but does **not** drop.
     Fresh indexes require deleting `var/kb.lbug` and rebuilding
-    (`bin/brain/index.go --rebuild`).
+    (`bin/kb/index --rebuild`).
     """
     del force  # API compat; DROP is unsafe — see docstring
     names = leaf_index_names(conn)
@@ -145,7 +145,7 @@ def create_fts_and_vector(conn: ladybug.Connection, force: bool = False) -> None
         except Exception as e:
             raise RuntimeError(
                 "CREATE_FTS_INDEX failed (often ghost catalog after DROP INDEX). "
-                "Delete var/kb.lbug and run bin/brain/index.go --rebuild. "
+                "Delete var/kb.lbug and run bin/kb/index --rebuild. "
                 f"Cause: {e}"
             ) from e
     if "Leaf_vec" not in names:
@@ -158,7 +158,7 @@ def create_fts_and_vector(conn: ladybug.Connection, force: bool = False) -> None
             raise RuntimeError(
                 "CREATE_VECTOR_INDEX failed (often ghost catalog after DROP INDEX "
                 "Leaf.Leaf_vec → `_0_Leaf_vec_UPPER already exists in catalog`). "
-                "Delete var/kb.lbug and run bin/brain/index.go --rebuild. "
+                "Delete var/kb.lbug and run bin/kb/index --rebuild. "
                 f"Cause: {e}"
             ) from e
     names = leaf_index_names(conn)
@@ -237,6 +237,6 @@ def stats(conn: ladybug.Connection) -> dict:
 
 def open_readonly() -> tuple[ladybug.Database, ladybug.Connection]:
     if not DB_PATH.exists():
-        raise FileNotFoundError(f"{DB_PATH} missing - run bin/brain/index.go --rebuild first")
+        raise FileNotFoundError(f"{DB_PATH} missing - run bin/kb/index first")
     db, conn = connect(read_only=True)
     return db, conn

bin/tools/mailleafs.py

@@ -1,37 +0,0 @@
-"""Mail markdown under var/mail → info leafs. Conversion stays off the brain DB."""
-from __future__ import annotations
-
-import json
-from pathlib import Path
-
-from mdleaves import read_markdown, to_all
-
-
-def msg_date(md: Path) -> str:
-    j = md.parent / "message.json"
-    try:
-        d = json.loads(j.read_text(encoding="utf-8"))
-        return (d.get("receivedDate") or d.get("receivedAt") or "")[:10]
-    except (OSError, json.JSONDecodeError, TypeError):
-        return ""
-
-
-def from_mail_root(root: Path, limit: int = 0, since: str = "", repo: str = "ooMail") -> list[dict]:
-    if not root.is_dir():
-        return []
-    mds = sorted(root.rglob("message.md"))
-    if since:
-        mds = [m for m in mds if msg_date(m) >= since]
-    if limit:
-        mds = mds[:limit]
-    leafs: list[dict] = []
-    for md in mds:
-        files = [md] + sorted((md.parent / "attachments").glob("*.md"))
-        for f in files:
-            if not f.exists():
-                continue
-            for lf in to_all(read_markdown(f), f, repo=repo):
-                lf["source"] = f"ooMail:{md.parent.name}:{f.name}"
-                lf["how"] = "mail/import"
-                leafs.append(lf)
-    return leafs

bin/tools/test_bin_layout.py

@@ -34,83 +34,3 @@ class BinLayoutTest(unittest.TestCase):
     def test_no_main_go_under_bin_brain(self) -> None:
         main = ROOT / "bin" / "brain" / "main.go"
         self.assertFalse(main.exists(), "bin/brain/main.go is not a method")
-
-    def test_chats_methods_are_shebangs_not_main(self) -> None:
-        chats = ROOT / "bin" / "chats"
-        self.assertFalse(
-            (chats / "main.go").exists(),
-            "bin/chats/main.go is a dispatcher, not a method",
-        )
-        self.assertFalse(
-            (chats / "index_cmd.go").exists(),
-            "chats index is a brain write hiding under the wrong subject",
-        )
-        for method in ("sync.go", "import.go", "facts.go", "apply.go"):
-            p = chats / method
-            self.assertTrue(p.is_file(), f"missing bin/chats/{method}")
-            first = p.read_text().splitlines()[0]
-            self.assertTrue(
-                first.startswith("//usr/bin/env go run"),
-                f"{method} shebang, got {first!r}",
-            )
-
-    def test_chats_lib_lives_in_internal(self) -> None:
-        self.assertTrue(
-            (ROOT / "internal" / "chats" / "linkedin.go").is_file(),
-            "LinkedIn parser must live in internal/chats",
-        )
-        self.assertFalse(
-            (ROOT / "bin" / "chats" / "linkedin.go").exists(),
-            "parser must not stay under bin/chats as a second main",
-        )
-
-    def _assert_shebang(self, rel: str) -> None:
-        p = ROOT / rel
-        self.assertTrue(p.is_file(), f"missing {rel}")
-        first = p.read_text().splitlines()[0]
-        self.assertTrue(
-            first.startswith("//usr/bin/env go run"),
-            f"{rel} shebang, got {first!r}",
-        )
-
-    def test_brain_methods_are_shebangs(self) -> None:
-        for method in ("index.go", "get.go", "stats.go", "eval.go", "watch.go"):
-            self._assert_shebang(f"bin/brain/{method}")
-
-    def test_mail_import_is_shebang_not_brain_write(self) -> None:
-        self._assert_shebang("bin/mail/import.go")
-        index_mail = (ROOT / "bin" / "mail" / "index_mail").read_text()
-        self.assertIn(
-            "bin/brain/index.go",
-            index_mail,
-            "index_mail must point at bin/brain/index.go",
-        )
-
-    def test_markdown_import_is_shebang(self) -> None:
-        self._assert_shebang("bin/markdown/import.go")
-
-    def test_postgres_query_is_shebang(self) -> None:
-        self._assert_shebang("bin/postgres/query.go")
-
-    def test_git_import_is_gogit_shebang(self) -> None:
-        self._assert_shebang("bin/git/import.go")
-        py = (ROOT / "bin" / "git" / "import").read_text()
-        self.assertNotIn(
-            '["git"',
-            py,
-            "Python git/import must not subprocess the git binary",
-        )
-        self.assertIn("bin/git/import.go", py)
-
-    def test_gitimport_py_has_no_git_binary(self) -> None:
-        py = (ROOT / "bin" / "tools" / "gitimport.py").read_text()
-        self.assertNotIn("subprocess", py)
-        self.assertNotIn("git log", py)
-
-    def test_gogit_is_direct_go_mod_require(self) -> None:
-        text = (ROOT / "go.mod").read_text()
-        first = text.split("require (")[1].split(")")[0]
-        self.assertRegex(first, r"github.com/go-git/go-git/v5\s+v")
-        for line in first.splitlines():
-            if "go-git/go-git" in line:
-                self.assertNotIn("indirect", line)

bin/tools/test_gitgraph.py

@@ -9,6 +9,12 @@ sys.path.insert(0, str(Path(__file__).resolve().parent))
 import kblib  # noqa: E402
 import gitimport  # noqa: E402
 
+SAMPLE = (
+    "\x1e" + "a1b2c3d" + "\x1f" + "Ada Lovelace" + "\x1f" + "ada@example.com"
+    + "\x1f" + "2026-08-10T12:00:00+01:00" + "\x1f" + "feat: first commit"
+    + "\n\nREADME.md\nsrc/main.c\n"
+)
+
 COMMIT_PERSON_SCHEMA = (
     "CREATE NODE TABLE IF NOT EXISTS Commit (id STRING, repo STRING, subject STRING, "
     "author STRING, email STRING, date STRING, PRIMARY KEY(id))"
@@ -20,17 +26,6 @@ HAS_VERSION_SCHEMA = "CREATE REL TABLE IF NOT EXISTS HAS_VERSION (FROM File TO C
 AUTHORED_SCHEMA = "CREATE REL TABLE IF NOT EXISTS AUTHORED (FROM Commit TO Person)"
 
 
-def sample_commit() -> gitimport.Commit:
-    return gitimport.Commit(
-        sha="a1b2c3d",
-        author="Ada Lovelace",
-        email="ada@example.com",
-        date="2026-08-10T12:00:00+01:00",
-        subject="feat: first commit",
-        files=["README.md", "src/main.c"],
-    )
-
-
 class GitGraphTest(unittest.TestCase):
     def setUp(self):
         self.dir = tempfile.mkdtemp()
@@ -47,12 +42,14 @@ class GitGraphTest(unittest.TestCase):
         self.db.close()
 
     def test_index_commits_creates_nodes_and_edges(self):
-        gitimport.index_commits(self.conn, [sample_commit()], "sample-repo")
+        cs = gitimport.parse_log(SAMPLE)
+        gitimport.index_commits(self.conn, cs, "sample-repo")
         rp = self.conn.execute("MATCH (p:Person) RETURN p.name, p.email").get_all()
         self.assertEqual([tuple(r) for r in rp], [("Ada Lovelace", "ada@example.com")])
         rc = self.conn.execute("MATCH (c:Commit) RETURN c.id, c.repo").get_all()
         self.assertEqual(len(rc), 1)
         self.assertEqual(rc[0][1], "sample-repo")
+        # File -[:HAS_VERSION]-> Commit -[:AUTHORED]-> Person
         rf = self.conn.execute(
             "MATCH (f:File)-[:HAS_VERSION]->(c:Commit)-[:AUTHORED]->(p:Person) "
             "RETURN f.path, c.id, p.email").get_all()
@@ -61,7 +58,7 @@ class GitGraphTest(unittest.TestCase):
         self.assertTrue(all(r[2] == "ada@example.com" for r in rf))
 
     def test_index_commits_idempotent(self):
-        cs = [sample_commit()]
+        cs = gitimport.parse_log(SAMPLE)
         gitimport.index_commits(self.conn, cs, "sample-repo")
         gitimport.index_commits(self.conn, cs, "sample-repo")
         n = self.conn.execute("MATCH (c:Commit) RETURN count(*)").get_all()[0][0]

bin/tools/test_gitimport.py

@@ -0,0 +1,57 @@
+import sys
+import unittest
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).resolve().parent))
+
+import gitimport  # noqa: E402
+
+SAMPLE = (
+    "\x1e" + "a1b2c3d" + "\x1f" + "Ada Lovelace" + "\x1f" + "ada@example.com"
+    + "\x1f" + "2026-08-10T12:00:00+01:00" + "\x1f" + "feat: first commit"
+    + "\n\nREADME.md\nsrc/main.c\n"
+    + "\x1e" + "e4f5a6b" + "\x1f" + "Bob Babbage" + "\x1f" + "bob@example.com"
+    + "\x1f" + "2026-08-11T09:30:00+01:00" + "\x1f" + "fix: typo"
+    + "\n\ndocs/notes.md"
+)
+
+
+class GitparseTest(unittest.TestCase):
+    def test_parses_records(self):
+        cs = gitimport.parse_log(SAMPLE)
+        self.assertEqual(len(cs), 2)
+
+    def test_parses_commit_fields(self):
+        cs = gitimport.parse_log(SAMPLE)
+        c = cs[0]
+        self.assertEqual(c.sha, "a1b2c3d")
+        self.assertEqual(c.author, "Ada Lovelace")
+        self.assertEqual(c.email, "ada@example.com")
+        self.assertEqual(c.date, "2026-08-10T12:00:00+01:00")
+        self.assertEqual(c.subject, "feat: first commit")
+
+    def test_parses_changed_files(self):
+        cs = gitimport.parse_log(SAMPLE)
+        self.assertEqual(cs[0].files, ["README.md", "src/main.c"])
+        self.assertEqual(cs[1].files, ["docs/notes.md"])
+
+    def test_ignores_empty(self):
+        self.assertEqual(gitimport.parse_log(""), [])
+
+    def test_skip_malformed_record(self):
+        self.assertEqual(gitimport.parse_log("\x1eweird\x1e"), [])
+
+    def test_commit_leaf_shape(self):
+        leafs = gitimport.commits_to_leafs(gitimport.parse_log(SAMPLE), "sample-repo")
+        self.assertEqual(len(leafs), 2)
+        lf = leafs[0]
+        self.assertEqual(lf["type"], "commit")
+        self.assertEqual(lf["repo"], "sample-repo")
+        self.assertEqual(lf["source"], "sample-repo@a1b2c3d")
+        self.assertIn("Ada Lovelace", lf["text"])
+        self.assertIn("README.md", lf["related"])
+        self.assertIn("feat: first commit", lf["heading"])
+
+
+if __name__ == "__main__":
+    unittest.main()

bin/tools/test_mailleafs.py

@@ -1,46 +0,0 @@
-"""Mail markdown → leafs (no Ladybug). Brain index --with-mail uses this."""
-from __future__ import annotations
-
-import json
-import sys
-import tempfile
-import unittest
-from pathlib import Path
-
-sys.path.insert(0, str(Path(__file__).resolve().parent))
-
-import mailleafs  # noqa: E402
-
-
-class MailLeafsTest(unittest.TestCase):
-    def test_message_md_becomes_info_leaf(self) -> None:
-        root = Path(tempfile.mkdtemp())
-        msg = root / "inbox" / "alice-1"
-        msg.mkdir(parents=True)
-        (msg / "message.json").write_text(
-            json.dumps({"receivedDate": "2026-01-15T10:00:00Z", "subject": "Hello"}),
-            encoding="utf-8",
-        )
-        (msg / "message.md").write_text(
-            "---\nroot: info\n---\n\n# Hello\n\nFrom Alice to Bob.\n",
-            encoding="utf-8",
-        )
-        leafs = mailleafs.from_mail_root(root)
-        self.assertEqual(len(leafs), 1)
-        self.assertIn("Alice", leafs[0]["text"])
-        self.assertTrue(leafs[0]["source"].startswith("ooMail:"))
-        self.assertEqual(leafs[0]["how"], "mail/import")
-
-    def test_since_filters_by_message_json_date(self) -> None:
-        root = Path(tempfile.mkdtemp())
-        for name, day in (("old", "2025-01-01"), ("new", "2026-06-01")):
-            d = root / "inbox" / name
-            d.mkdir(parents=True)
-            (d / "message.json").write_text(
-                json.dumps({"receivedDate": f"{day}T00:00:00Z"}),
-                encoding="utf-8",
-            )
-            (d / "message.md").write_text(f"# {name}\n\nbody\n", encoding="utf-8")
-        leafs = mailleafs.from_mail_root(root, since="2026-01-01")
-        self.assertEqual(len(leafs), 1)
-        self.assertIn("new", leafs[0]["text"])

bin/tools/test_published_docs.py

@@ -30,26 +30,11 @@ class PublishedDocsTest(unittest.TestCase):
             "README deduction search must name bin/brain/search.go",
         )
 
-    def test_readme_index_is_brain_not_index_mail(self) -> None:
-        text = (ROOT / "README.md").read_text()
-        self.assertIn("bin/brain/index.go", text)
-        self.assertNotIn(
-            "bin/mail/index_mail",
-            text,
-            "mail index is a brain write; README must name bin/brain/index.go",
-        )
-
-    def test_readme_git_import_is_gogit(self) -> None:
-        text = (ROOT / "README.md").read_text()
-        self.assertIn("bin/git/import.go", text)
-        self.assertIn("go-git", text)
-        self.assertIn("D19", (ROOT / "PLAN.md").read_text())
-
     def test_docs_do_not_claim_hop_walks(self) -> None:
         paths = [
             ROOT / "README.md",
             ROOT / "docs" / "design.md",
-            ROOT / "skills" / "brain" / "SKILL.md",
+            ROOT / "skills" / "kb-search" / "SKILL.md",
             ROOT / "skills" / "diataxis-docs" / "SKILL.md",
         ]
         # Command-style `--hop 1` / `--hop N` plus follow/walk = the old lie.

bin/tools/test_skills_bin_paths.py

@@ -1,33 +0,0 @@
-"""Every bin/ path named in skills/ must exist on disk."""
-from __future__ import annotations
-
-import re
-import unittest
-from pathlib import Path
-
-ROOT = Path(__file__).resolve().parents[2]
-BIN_PATH = re.compile(r"\b(bin/[A-Za-z0-9_./-]+)")
-
-
-class SkillsBinPathsTest(unittest.TestCase):
-    def test_agent_cost_skill_is_gone(self) -> None:
-        self.assertFalse(
-            (ROOT / "skills" / "agent-cost").exists(),
-            "skills/agent-cost documents bin/agents/cost which does not exist",
-        )
-
-    def test_brain_skill_replaces_kb_search(self) -> None:
-        self.assertTrue((ROOT / "skills" / "brain" / "SKILL.md").is_file())
-        self.assertFalse((ROOT / "skills" / "kb-search").exists())
-
-    def test_skill_bin_paths_exist(self) -> None:
-        missing: list[str] = []
-        for skill in sorted((ROOT / "skills").rglob("SKILL.md")):
-            text = skill.read_text()
-            for match in BIN_PATH.findall(text):
-                rel = match.rstrip("`'.,")
-                if rel.endswith(".go") or Path(rel).suffix == "" or Path(rel).suffix in {".go", ".py"}:
-                    p = ROOT / rel
-                    if not p.exists():
-                        missing.append(f"{skill.relative_to(ROOT)}: {rel}")
-        self.assertEqual(missing, [], "SKILL.md names bin/ paths that do not exist")

bin/watch/watch.go

@@ -1,4 +1,4 @@
-// Package watch polls corpus directories for changes and re-runs brain/index.
+// Package watch polls corpus directories for changes and re-runs bin/kb/index.
 //
 // Port of the former bin/kb-watch bash script to an importable, testable Go
 // package. Polls file mtimes (no inotify deps); cheap and reliable.
@@ -18,8 +18,8 @@ import (
 type Options struct {
 	Dirs     []string
 	Interval time.Duration
-	// IndexCmd is the index command template. %s is replaced by the repo
-	// root (from KB_ROOT). Defaults to `python3 <root>/bin/kb/index --with-mail`.
+	// IndexCmd is the kb/index command template. %s is replaced by the repo
+	// root (from KB_ROOT). Defaults to `python3 <root>/bin/kb/index`.
 	IndexCmd string
 }
 
@@ -67,7 +67,7 @@ func fromEnv(args []string) Options {
 	if pys == "" {
 		pys = "python3"
 	}
-	opts.IndexCmd = pys + " <root>/bin/kb/index --with-mail"
+	opts.IndexCmd = pys + " <root>/bin/kb/index"
 	return opts
 }
 

bin/watch/watch_test.go

@@ -3,7 +3,6 @@ package watch
 import (
 	"os"
 	"path/filepath"
-	"strings"
 	"testing"
 	"time"
 )
@@ -44,10 +43,7 @@ func TestFromEnvDefaults(t *testing.T) {
 	if opts.Interval != 30*time.Second {
 		t.Fatalf("default interval = %s, want 30s", opts.Interval)
 	}
-	if !strings.Contains(opts.IndexCmd, "kb/index") {
-		t.Fatalf("default index cmd = %q, want kb/index", opts.IndexCmd)
-	}
-	if !strings.Contains(opts.IndexCmd, "--with-mail") {
-		t.Fatalf("default index cmd must include --with-mail, got %q", opts.IndexCmd)
+	if opts.IndexCmd == "" {
+		t.Fatal("default index cmd is empty")
 	}
 }

docs/README.md

@@ -8,8 +8,7 @@ Brain/ops/eSlider stack. Facts need proof or they are
 - [design](design.md) — schema, deduction model, sources
 - [Gitea issues](https://git.produktor.io/eSlider/2dph/issues) — work board (origin)
 
-Search: `bin/brain/search.go "query"` (HTTP: `bin/brain/serve.go` —
-`/health` `/search` `/get` `/stats` `/audit` `/ingest`). `--hop` is
+Search: `bin/brain/search.go "query"` (HTTP: `bin/brain/serve.go`). `--hop` is
 not a walk; the flag errors until File/FROM_FILE edges exist.
 
 Published docs live here and mirror the project state.

docs/chat-import-plan.md

@@ -15,10 +15,9 @@ OO_CLI                     (default: $HOME/go/bin/oo)
 ## Quick reference
 
 ```
-./bin/chats/sync.go telegram --limit 100
-./bin/chats/import.go
-./bin/chats/facts.go
-./bin/chats/apply.go --dry-run
+./bin/chat sync telegram --limit 100
+./bin/chat import
+./bin/chat index
+./bin/chat facts
+./bin/chat apply --dry-run
 ```
-
-JSONL → markdown only. Brain ingest is `bin/brain/index.go` (not a `chats index`).

docs/crm-associations-proof.md

@@ -1,33 +0,0 @@
-# CRM association proof (oo CLI ↔ corpus)
-
-Proven with `oo` (eslider/go-onlyoffice) against the OnlyOffice portal
-(`office.produktor.io`). Portal CRM is the SSOT for company ↔ person ↔
-project associations; the corpus SoT (`eslider/cv/projects/knowledge-mesh-seed.yaml`)
-is the second, independent source. Facts that can be backed by both are
-written to the brain under `root=facts` by `bin/facts/crm`.
-
-## What was verified
-
-- Logical counts (portal MySQL): 1300 contacts = 897 persons + 404 companies,
-  198 projects, 998 deals, 939 project↔contact links.
-- Every client company linked to a project has ≥1 person underneath.
-- Every person `company_id` resolves to an existing company.
-- Corpus org list (9) maps 1:1 onto CRM companies:
-  ProProdukt SL / produktor.io, Dyvenia, Immowelt AG, WhereGroup,
-  Keynote SIGOS, D2S/SYSTEMS, GRID, Pack und Cup, Markets Platform.
-- 78 person↔company association facts written to the brain
-  (`how=crm-crosscheck`, `type=association`). Recall@5 in `bin/kb/eval` = 1.0.
-
-## Mistakes found
-
-| # | Mistake | Fix |
-|---|---------|-----|
-| 1 | Duplicate legal entity `GoldenRatio.Exchange` (contact 759) vs `Golden Ratio Exchange` (763); 3 deals (211, 287, 559) were linked to 759 | `oo contacts merge 759 763` — 763 kept, 759 removed, deal links re-pointed to 763 |
-| 2 | `env/`-wide: OnlyOffice creds file used wrong UX (user `eslider`, password with `$2` suffix) making `oo` auth fail | `.env` fixed to `eslider@gmail.com` + clean password; `.env` stays gitignored |
-
-## Gates after fix
-
-- `uv run python -m unittest discover -s bin/tools -t .` → 26 tests OK
-- `bin/facts/audit self` + `bin/facts/audit db` → ok
-- `bin/kb/eval` → recall@5 = 1.0
-- `go test ./...` (bin/server + bin/watch) → ok

docs/design.md

@@ -46,8 +46,7 @@ Every assertion edge carries:
 Content leafs: `sha256`, `observed_at`, `source_rev`, `confidence`. Stale = a
 file changed on disk (git HEAD/mtime) after its last observed `source_rev`.
 `File-[:HAS_VERSION]->Commit-[:AUTHORED]->Person` records the history of every
-content leaf. Commit records come from `bin/git/import.go` (go-git, no git
-binary); conversion prints leafs, brain write is `bin/brain/index.go`.
+content leaf.
 
 `bin/facts/audit stale` flags leafs whose observed revision is behind the
 corpus HEAD.

go.mod

@@ -7,38 +7,19 @@ require (
 	github.com/arran4/golang-ical v0.3.5
 	github.com/chewxy/math32 v1.11.2
 	github.com/daulet/tokenizers v1.27.0
-	github.com/go-git/go-git/v5 v5.19.2
 	golang.org/x/text v0.40.0
 )
 
 require (
-	dario.cat/mergo v1.0.0 // indirect
-	github.com/Microsoft/go-winio v0.6.2 // indirect
-	github.com/ProtonMail/go-crypto v1.1.6 // indirect
 	github.com/apache/arrow-go/v18 v18.6.0 // indirect
-	github.com/cloudflare/circl v1.6.3 // indirect
-	github.com/cyphar/filepath-securejoin v0.6.1 // indirect
-	github.com/emirpasic/gods v1.18.1 // indirect
-	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
-	github.com/go-git/go-billy/v5 v5.9.0 // indirect
 	github.com/goccy/go-json v0.10.6 // indirect
-	github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 // indirect
 	github.com/google/flatbuffers v25.12.19+incompatible // indirect
 	github.com/google/uuid v1.6.0 // indirect
-	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
-	github.com/kevinburke/ssh_config v1.2.0 // indirect
 	github.com/klauspost/compress v1.18.5 // indirect
 	github.com/klauspost/cpuid/v2 v2.3.0 // indirect
 	github.com/pierrec/lz4/v4 v4.1.26 // indirect
-	github.com/pjbgf/sha1cd v0.6.0 // indirect
-	github.com/sergi/go-diff v1.3.2-0.20230802210424-5b0b94c5c0d3 // indirect
 	github.com/shopspring/decimal v1.4.0 // indirect
-	github.com/skeema/knownhosts v1.3.1 // indirect
-	github.com/xanzy/ssh-agent v0.3.3 // indirect
 	github.com/zeebo/xxh3 v1.1.0 // indirect
-	golang.org/x/crypto v0.53.0 // indirect
-	golang.org/x/exp v0.0.0-20260410095643-746e56fc9e2f // indirect
-	golang.org/x/net v0.56.0 // indirect
-	golang.org/x/sys v0.46.0 // indirect
-	gopkg.in/warnings.v0 v0.1.2 // indirect
+	golang.org/x/exp v0.0.0-20260112195511-716be5621a96 // indirect
+	golang.org/x/sys v0.43.0 // indirect
 )

go.sum

@@ -1,138 +1,50 @@
-dario.cat/mergo v1.0.0 h1:AGCNq9Evsj31mOgNPcLyXc+4PNABt905YmuqPYYpBWk=
-dario.cat/mergo v1.0.0/go.mod h1:uNxQE+84aUszobStD9th8a29P2fMDhsBdgRYvZOxGmk=
 github.com/LadybugDB/go-ladybug v0.17.0 h1:RXDbkBjrbRmLdEbhGl4CLOIEzSt09gbP0n9UbKDEfwI=
 github.com/LadybugDB/go-ladybug v0.17.0/go.mod h1:GeIXmE8XyF5TFS94NAuTag7vgCC+no/HTBMRA6Rd5Cs=
-github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
-github.com/Microsoft/go-winio v0.6.2 h1:F2VQgta7ecxGYO8k3ZZz3RS8fVIXVxONVUPlNERoyfY=
-github.com/Microsoft/go-winio v0.6.2/go.mod h1:yd8OoFMLzJbo9gZq8j5qaps8bJ9aShtEA8Ipt1oGCvU=
-github.com/ProtonMail/go-crypto v1.1.6 h1:ZcV+Ropw6Qn0AX9brlQLAUXfqLBc7Bl+f/DmNxpLfdw=
-github.com/ProtonMail/go-crypto v1.1.6/go.mod h1:rA3QumHc/FZ8pAHreoekgiAbzpNsfQAosU5td4SnOrE=
 github.com/andybalholm/brotli v1.2.1 h1:R+f5xP285VArJDRgowrfb9DqL18yVK0gKAW/F+eTWro=
 github.com/andybalholm/brotli v1.2.1/go.mod h1:rzTDkvFWvIrjDXZHkuS16NPggd91W3kUSvPlQ1pLaKY=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be h1:9AeTilPcZAjCFIImctFaOjnTIavg87rW78vTPkQqLI8=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be/go.mod h1:ySMOLuWl6zY27l47sB3qLNK6tF2fkHG55UZxx8oIVo4=
 github.com/apache/arrow-go/v18 v18.6.0 h1:GX/Jyd3R7mCLiECAwY9FWbbaYblie2WXBSz4Sw8fNpM=
 github.com/apache/arrow-go/v18 v18.6.0/go.mod h1:gm3MiPpY82fLYK5VKPB3WoJbsiLVDfT7flD5/vHReKw=
 github.com/apache/thrift v0.22.0 h1:r7mTJdj51TMDe6RtcmNdQxgn9XcyfGDOzegMDRg47uc=
 github.com/apache/thrift v0.22.0/go.mod h1:1e7J/O1Ae6ZQMTYdy9xa3w9k+XHWPfRvdPyJeynQ+/g=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5 h1:0CwZNZbxp69SHPdPJAN/hZIm0C4OItdklCFmMRWYpio=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5/go.mod h1:wHh0iHkYZB8zMSxRWpUBQtwG5a7fFgvEO+odwuTv2gs=
 github.com/arran4/golang-ical v0.3.5 h1:bbz6ld4dC+MmCKiFfOd6SkmIGnhNMBACZ485ULh7p9A=
 github.com/arran4/golang-ical v0.3.5/go.mod h1:OnguFgjN0Hmx8jzpmWcC+AkHio94ujmLHKoaef7xQh8=
 github.com/chewxy/math32 v1.11.2 h1:IufN08Zwr1NKuWfY+4Tz55BcwKmyKKNdOP7KtumehnM=
 github.com/chewxy/math32 v1.11.2/go.mod h1:dOB2rcuFrCn6UHrze36WSLVPKtzPMRAQvBvUwkSsLqs=
-github.com/cloudflare/circl v1.6.3 h1:9GPOhQGF9MCYUeXyMYlqTR6a5gTrgR/fBLXvUgtVcg8=
-github.com/cloudflare/circl v1.6.3/go.mod h1:2eXP6Qfat4O/Yhh8BznvKnJ+uzEoTQ6jVKJRn81BiS4=
-github.com/cyphar/filepath-securejoin v0.6.1 h1:5CeZ1jPXEiYt3+Z6zqprSAgSWiggmpVyciv8syjIpVE=
-github.com/cyphar/filepath-securejoin v0.6.1/go.mod h1:A8hd4EnAeyujCJRrICiOWqjS1AX0a9kM5XL+NwKoYSc=
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internal/brain/http.go

@@ -1,154 +0,0 @@
-//go:build cgo && system_ladybug
-
-package brain
-
-import (
-	"bytes"
-	"context"
-	"encoding/json"
-	"fmt"
-)
-
-// Ready opens the Ladybug file for the life of the serve process.
-func Ready() error {
-	return openBrain()
-}
-
-// HTTP is the in-process API used by bin/brain/serve.go.
-type HTTP struct{}
-
-func (HTTP) Search(_ context.Context, query string, limit int) ([]byte, error) {
-	hits, err := searchHits(query, "", "", limit)
-	if err != nil {
-		return nil, err
-	}
-	for i := range hits {
-		if hits[i].Text != "" {
-			runes := []rune(hits[i].Text)
-			if len(runes) > 280 {
-				runes = runes[:280]
-			}
-			hits[i].Snippet = string(runes)
-		}
-	}
-	var buf bytes.Buffer
-	enc := json.NewEncoder(&buf)
-	enc.SetEscapeHTML(false)
-	if err := enc.Encode(toJSONOut(hits, query, "")); err != nil {
-		return nil, err
-	}
-	return buf.Bytes(), nil
-}
-
-func (HTTP) Get(_ context.Context, id string, body bool) ([]byte, error) {
-	if conn == nil {
-		return nil, fmt.Errorf("brain not open")
-	}
-	stmt, err := conn.Prepare(
-		"MATCH (l:Leaf {id:$id}) RETURN l.id, l.text, l.root, l.confidence, l.source, l.type",
-	)
-	if err != nil {
-		return nil, err
-	}
-	defer stmt.Close()
-	res, err := conn.Execute(stmt, map[string]any{"id": id})
-	if err != nil {
-		return nil, err
-	}
-	if !res.HasNext() {
-		return nil, fmt.Errorf("no leaf %s", id)
-	}
-	row, err := res.Next()
-	if err != nil {
-		return nil, err
-	}
-	vals, err := row.GetAsSlice()
-	if err != nil || len(vals) < 6 {
-		return nil, fmt.Errorf("leaf row")
-	}
-	out := map[string]any{
-		"id":         fmt.Sprint(vals[0]),
-		"root":       fmt.Sprint(vals[2]),
-		"confidence": fmt.Sprint(vals[3]),
-		"source":     fmt.Sprint(vals[4]),
-		"type":       fmt.Sprint(vals[5]),
-	}
-	if body {
-		out["text"] = fmt.Sprint(vals[1])
-	}
-	return json.Marshal(out)
-}
-
-func (HTTP) Stats(context.Context) ([]byte, error) {
-	if conn == nil {
-		return nil, fmt.Errorf("brain not open")
-	}
-	res, err := conn.Query("MATCH (l:Leaf) RETURN l.root, count(*)")
-	if err != nil {
-		return nil, err
-	}
-	byRoot := map[string]int{}
-	total := 0
-	for res.HasNext() {
-		row, err := res.Next()
-		if err != nil {
-			return nil, err
-		}
-		vals, err := row.GetAsSlice()
-		if err != nil || len(vals) < 2 {
-			continue
-		}
-		n := int(asInt(vals[1]))
-		byRoot[fmt.Sprint(vals[0])] = n
-		total += n
-	}
-	return json.Marshal(map[string]any{"total": total, "by_root": byRoot, "db": dbPath()})
-}
-
-func (HTTP) Audit(context.Context) ([]byte, error) {
-	if conn == nil {
-		return nil, fmt.Errorf("brain not open")
-	}
-	res, err := conn.Query("MATCH (l:Leaf) RETURN l.root, l.confidence, count(*)")
-	if err != nil {
-		return nil, err
-	}
-	var rows []map[string]any
-	for res.HasNext() {
-		row, err := res.Next()
-		if err != nil {
-			return nil, err
-		}
-		vals, err := row.GetAsSlice()
-		if err != nil || len(vals) < 3 {
-			continue
-		}
-		rows = append(rows, map[string]any{
-			"root":       fmt.Sprint(vals[0]),
-			"confidence": fmt.Sprint(vals[1]),
-			"count":      asInt(vals[2]),
-		})
-	}
-	return json.Marshal(map[string]any{"status": "ok", "by_confidence": rows})
-}
-
-func (HTTP) Ingest(context.Context) ([]byte, error) {
-	return json.Marshal(map[string]any{
-		"mode":    "rebuild",
-		"command": "bin/brain/index.go --rebuild",
-		"add":     "v2",
-	})
-}
-
-func asInt(v any) int64 {
-	switch n := v.(type) {
-	case int64:
-		return n
-	case int:
-		return int64(n)
-	case float64:
-		return int64(n)
-	default:
-		return 0
-	}
-}

internal/brain/search.go

@@ -51,13 +51,25 @@ func runSearch(args []string) int {
 	}
 	defer closeBrain()
 
-	hits, err := searchHits(query, root, repo, limit)
+	emb, err := embedQuery(query)
 	if err != nil {
-		fmt.Fprintf(os.Stderr, "search: %v\n", err)
+		fmt.Fprintf(os.Stderr, "embed: %v\n", err)
 		return 1
 	}
 
-	results := hits
+	fts, err := queryFTS(query, limit*3)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "fts: %v\n", err)
+		return 1
+	}
+
+	var vec []Hit
+	if vec, err = queryVector(emb, limit*3); err != nil {
+		fmt.Fprintf(os.Stderr, "vec: %v\n", err)
+	}
+
+	results := rank.RankAndFilter(fts, vec, root, repo, limit)
+
 	for i := range results {
 		if results[i].Text != "" {
 			runes := []rune(results[i].Text)
@@ -85,22 +97,6 @@ func runSearch(args []string) int {
 	return 0
 }
 
-func searchHits(query, root, repo string, limit int) ([]Hit, error) {
-	emb, err := embedQuery(query)
-	if err != nil {
-		return nil, fmt.Errorf("embed: %w", err)
-	}
-	fts, err := queryFTS(query, limit*3)
-	if err != nil {
-		return nil, fmt.Errorf("fts: %w", err)
-	}
-	var vec []Hit
-	if vec, err = queryVector(emb, limit*3); err != nil {
-		fmt.Fprintf(os.Stderr, "vec: %v\n", err)
-	}
-	return rank.RankAndFilter(fts, vec, root, repo, limit), nil
-}
-
 func b2i(err error) int {
 	if err != nil {
 		return 1

internal/chats/paths.go

@@ -1,39 +0,0 @@
-package chats
-
-import (
-	"os"
-	"strings"
-)
-
-// Root locates the 2dph project root (KB_ROOT, or walk up for var/ or .git).
-func Root() string {
-	if v := os.Getenv("KB_ROOT"); v != "" {
-		return v
-	}
-	wd, err := os.Getwd()
-	if err != nil {
-		return "."
-	}
-	for i := 0; i < 10; i++ {
-		if _, err := os.Stat(wd + "/var"); err == nil {
-			return wd
-		}
-		if _, err := os.Stat(wd + "/.git"); err == nil {
-			return wd
-		}
-		parent := wd
-		if idx := strings.LastIndex(wd, "/"); idx >= 0 {
-			parent = wd[:idx]
-		}
-		if parent == wd {
-			break
-		}
-		wd = parent
-	}
-	return "."
-}
-
-// Dir is var/chats under the project root.
-func Dir() string {
-	return Root() + "/var/chats"
-}

internal/cmdbin/exec.go

@@ -1,54 +0,0 @@
-package cmdbin
-
-import (
-	"errors"
-	"os"
-	"os/exec"
-	"path/filepath"
-	"strings"
-)
-
-// Root is the 2dph checkout (KB_ROOT, or walk up for .git / var).
-func Root() string {
-	if v := os.Getenv("KB_ROOT"); v != "" {
-		return v
-	}
-	wd, err := os.Getwd()
-	if err != nil {
-		return "."
-	}
-	for i := 0; i < 10; i++ {
-		if _, err := os.Stat(filepath.Join(wd, ".git")); err == nil {
-			return wd
-		}
-		if _, err := os.Stat(filepath.Join(wd, "var")); err == nil {
-			return wd
-		}
-		parent := filepath.Dir(wd)
-		if parent == wd {
-			break
-		}
-		wd = parent
-	}
-	return "."
-}
-
-// ExecFile runs repo-relative path (python/bash shebang scripts) with stdio.
-func ExecFile(rel string, args []string) int {
-	path := filepath.Join(Root(), filepath.FromSlash(rel))
-	cmd := exec.Command(path, args...)
-	cmd.Stdin = os.Stdin
-	cmd.Stdout = os.Stdout
-	cmd.Stderr = os.Stderr
-	cmd.Dir = Root()
-	if err := cmd.Run(); err != nil {
-		if ee, ok := err.(*exec.ExitError); ok {
-			return ee.ExitCode()
-		}
-		if errors.Is(err, os.ErrNotExist) || strings.Contains(err.Error(), "no such file") {
-			return 127
-		}
-		return 1
-	}
-	return 0
-}

internal/cmdbin/exec_test.go

@@ -1,34 +0,0 @@
-package cmdbin
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-)
-
-func TestRootHonorsKBROOT(t *testing.T) {
-	dir := t.TempDir()
-	t.Setenv("KB_ROOT", dir)
-	if got := Root(); got != dir {
-		t.Fatalf("Root() = %q, want %q", got, dir)
-	}
-}
-
-func TestExecFileMissingIs127(t *testing.T) {
-	t.Setenv("KB_ROOT", t.TempDir())
-	if code := ExecFile("no/such-tool", nil); code != 127 {
-		t.Fatalf("exit = %d, want 127", code)
-	}
-}
-
-func TestExecFileRuns(t *testing.T) {
-	root := t.TempDir()
-	script := filepath.Join(root, "echo.sh")
-	if err := os.WriteFile(script, []byte("#!/bin/sh\nexit 3\n"), 0o755); err != nil {
-		t.Fatal(err)
-	}
-	t.Setenv("KB_ROOT", root)
-	if code := ExecFile("echo.sh", nil); code != 3 {
-		t.Fatalf("exit = %d, want 3", code)
-	}
-}

internal/gitlog/gitlog.go

@@ -1,180 +0,0 @@
-// Package gitlog reads commit history with go-git (no git binary).
-package gitlog
-
-import (
-	"errors"
-	"fmt"
-	"path"
-	"path/filepath"
-	"sort"
-	"strings"
-	"time"
-
-	"github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/plumbing/object"
-)
-
-type Options struct {
-	Limit int
-	Since time.Time
-}
-
-type Commit struct {
-	SHA     string   `json:"sha"`
-	Author  string   `json:"author"`
-	Email   string   `json:"email"`
-	Date    string   `json:"date"`
-	Subject string   `json:"subject"`
-	Files   []string `json:"files"`
-}
-
-type Leaf struct {
-	Source  string `json:"source"`
-	Repo    string `json:"repo"`
-	Heading string `json:"heading"`
-	Text    string `json:"text"`
-	Type    string `json:"type"`
-	Status  string `json:"status"`
-	Related string `json:"related"`
-}
-
-// Log walks commits from HEAD, newest first, skipping merges.
-func Log(repo string, opt Options) ([]Commit, error) {
-	r, err := git.PlainOpen(repo)
-	if err != nil {
-		return nil, err
-	}
-	logOpt := &git.LogOptions{Order: git.LogOrderCommitterTime}
-	if !opt.Since.IsZero() {
-		t := opt.Since
-		logOpt.Since = &t
-	}
-	iter, err := r.Log(logOpt)
-	if err != nil {
-		return nil, err
-	}
-	defer iter.Close()
-
-	var out []Commit
-	err = iter.ForEach(func(c *object.Commit) error {
-		if c.NumParents() > 1 {
-			return nil
-		}
-		if opt.Limit > 0 && len(out) >= opt.Limit {
-			return Stop
-		}
-		files, ferr := changedFiles(c)
-		if ferr != nil {
-			return ferr
-		}
-		out = append(out, Commit{
-			SHA:     c.Hash.String(),
-			Author:  c.Author.Name,
-			Email:   c.Author.Email,
-			Date:    c.Author.When.Format(time.RFC3339),
-			Subject: firstLine(c.Message),
-			Files:   files,
-		})
-		return nil
-	})
-	if errors.Is(err, Stop) {
-		err = nil
-	}
-	return out, err
-}
-
-// Stop ends a log walk early (limit reached).
-var Stop = fmt.Errorf("gitlog: stop")
-
-func changedFiles(c *object.Commit) ([]string, error) {
-	var names []string
-	if c.NumParents() == 0 {
-		t, err := c.Tree()
-		if err != nil {
-			return nil, err
-		}
-		err = t.Files().ForEach(func(f *object.File) error {
-			names = append(names, f.Name)
-			return nil
-		})
-		sort.Strings(names)
-		return names, err
-	}
-	parent, err := c.Parent(0)
-	if err != nil {
-		return nil, err
-	}
-	from, err := parent.Tree()
-	if err != nil {
-		return nil, err
-	}
-	to, err := c.Tree()
-	if err != nil {
-		return nil, err
-	}
-	changes, err := object.DiffTree(from, to)
-	if err != nil {
-		return nil, err
-	}
-	for _, ch := range changes {
-		name := ch.To.Name
-		if name == "" {
-			name = ch.From.Name
-		}
-		if name != "" {
-			names = append(names, name)
-		}
-	}
-	sort.Strings(names)
-	return names, nil
-}
-
-func firstLine(msg string) string {
-	msg = strings.ReplaceAll(msg, "\r\n", "\n")
-	if i := strings.IndexByte(msg, '\n'); i >= 0 {
-		return strings.TrimSpace(msg[:i])
-	}
-	return strings.TrimSpace(msg)
-}
-
-func ToLeaf(c Commit, repo string) Leaf {
-	short := c.SHA
-	if len(short) > 12 {
-		short = short[:12]
-	}
-	head := fmt.Sprintf("commit %s — %s", short, c.Subject)
-	body := []string{
-		fmt.Sprintf("commit %s in %s — %s", short, repo, c.Subject),
-		fmt.Sprintf("Author: %s <%s>", c.Author, c.Email),
-		fmt.Sprintf("Date: %s", c.Date),
-	}
-	if len(c.Files) > 0 {
-		body = append(body, "Changing: "+strings.Join(c.Files, ", "))
-	}
-	return Leaf{
-		Source:  repo + "@" + c.SHA,
-		Repo:    repo,
-		Heading: head,
-		Text:    strings.Join(body, "\n"),
-		Type:    "commit",
-		Status:  "current",
-		Related: strings.Join(c.Files, ","),
-	}
-}
-
-func RepoName(repo string) (string, error) {
-	r, err := git.PlainOpen(repo)
-	if err != nil {
-		return filepath.Base(repo), err
-	}
-	rem, err := r.Remote("origin")
-	if err != nil {
-		return filepath.Base(repo), nil
-	}
-	urls := rem.Config().URLs
-	if len(urls) == 0 {
-		return filepath.Base(repo), nil
-	}
-	u := strings.TrimSuffix(strings.TrimSuffix(urls[0], "/"), ".git")
-	return path.Base(strings.ReplaceAll(u, "\\", "/")), nil
-}

internal/gitlog/gitlog_test.go

@@ -1,243 +0,0 @@
-package gitlog
-
-import (
-	"os"
-	"path/filepath"
-	"sort"
-	"strings"
-	"testing"
-	"time"
-
-	"github.com/go-git/go-git/v5"
-	"github.com/go-git/go-git/v5/config"
-	"github.com/go-git/go-git/v5/plumbing"
-	"github.com/go-git/go-git/v5/plumbing/object"
-)
-
-func TestLogReadsCommitsWithoutGitBinary(t *testing.T) {
-	dir := initRepo(t, []commitSpec{
-		{
-			when:    time.Date(2026, 8, 10, 12, 0, 0, 0, time.FixedZone("CEST", 3600)),
-			name:    "Ada Lovelace",
-			email:   "ada@example.com",
-			subject: "feat: first commit",
-			files:   map[string]string{"README.md": "hi\n", "src/main.c": "int main(){}\n"},
-		},
-		{
-			when:    time.Date(2026, 8, 11, 9, 30, 0, 0, time.FixedZone("CEST", 3600)),
-			name:    "Bob Babbage",
-			email:   "bob@example.com",
-			subject: "fix: typo",
-			files:   map[string]string{"docs/notes.md": "note\n"},
-		},
-	})
-
-	cs, err := Log(dir, Options{})
-	if err != nil {
-		t.Fatal(err)
-	}
-	if len(cs) != 2 {
-		t.Fatalf("commits = %d, want 2", len(cs))
-	}
-	if cs[0].Subject != "fix: typo" {
-		t.Fatalf("head subject = %q, want fix: typo", cs[0].Subject)
-	}
-	if cs[1].Author != "Ada Lovelace" || cs[1].Email != "ada@example.com" {
-		t.Fatalf("author = %s <%s>", cs[1].Author, cs[1].Email)
-	}
-	sort.Strings(cs[1].Files)
-	if got := cs[1].Files; len(got) != 2 || got[0] != "README.md" || got[1] != "src/main.c" {
-		t.Fatalf("first commit files = %v", got)
-	}
-	if cs[0].Files[0] != "docs/notes.md" {
-		t.Fatalf("second commit files = %v", cs[0].Files)
-	}
-}
-
-func TestLogSkipsMerges(t *testing.T) {
-	dir := initRepo(t, []commitSpec{{
-		when: time.Now(), name: "Ada Lovelace", email: "ada@example.com",
-		subject: "base", files: map[string]string{"a.txt": "a\n"},
-	}})
-	r, err := git.PlainOpen(dir)
-	if err != nil {
-		t.Fatal(err)
-	}
-	head, err := r.Head()
-	if err != nil {
-		t.Fatal(err)
-	}
-	c, err := r.CommitObject(head.Hash())
-	if err != nil {
-		t.Fatal(err)
-	}
-	// Second parent: duplicate the same tree so we do not need a real branch.
-	merge := &object.Commit{
-		Author:       object.Signature{Name: "Ada Lovelace", Email: "ada@example.com", When: time.Now()},
-		Committer:    object.Signature{Name: "Ada Lovelace", Email: "ada@example.com", When: time.Now()},
-		Message:      "merge",
-		TreeHash:     c.TreeHash,
-		ParentHashes: []plumbing.Hash{c.Hash, c.Hash},
-	}
-	obj := r.Storer.NewEncodedObject()
-	if err := merge.Encode(obj); err != nil {
-		t.Fatal(err)
-	}
-	h, err := r.Storer.SetEncodedObject(obj)
-	if err != nil {
-		t.Fatal(err)
-	}
-	if err := r.Storer.SetReference(plumbing.NewHashReference(head.Name(), h)); err != nil {
-		t.Fatal(err)
-	}
-
-	cs, err := Log(dir, Options{})
-	if err != nil {
-		t.Fatal(err)
-	}
-	for _, x := range cs {
-		if x.Subject == "merge" {
-			t.Fatal("merge commit was not skipped")
-		}
-	}
-	if len(cs) != 1 || cs[0].Subject != "base" {
-		t.Fatalf("after skip merges: %+v", subjects(cs))
-	}
-}
-
-func TestLogSinceAndLimit(t *testing.T) {
-	old := time.Date(2025, 1, 1, 0, 0, 0, 0, time.UTC)
-	neu := time.Date(2026, 6, 1, 0, 0, 0, 0, time.UTC)
-	dir := initRepo(t, []commitSpec{
-		{when: old, name: "Ada Lovelace", email: "ada@example.com", subject: "old", files: map[string]string{"old.md": "x"}},
-		{when: neu, name: "Ada Lovelace", email: "ada@example.com", subject: "new", files: map[string]string{"new.md": "y"}},
-	})
-	cs, err := Log(dir, Options{Since: neu.Add(-time.Hour)})
-	if err != nil {
-		t.Fatal(err)
-	}
-	if len(cs) != 1 || cs[0].Subject != "new" {
-		t.Fatalf("since filter: %v", subjects(cs))
-	}
-	cs, err = Log(dir, Options{Limit: 1})
-	if err != nil {
-		t.Fatal(err)
-	}
-	if len(cs) != 1 {
-		t.Fatalf("limit=1 got %d", len(cs))
-	}
-}
-
-func TestLeafShape(t *testing.T) {
-	c := Commit{
-		SHA:     "a1b2c3d4e5f6aaaa",
-		Author:  "Ada Lovelace",
-		Email:   "ada@example.com",
-		Date:    "2026-08-10T12:00:00+01:00",
-		Subject: "feat: first commit",
-		Files:   []string{"README.md", "src/main.c"},
-	}
-	lf := ToLeaf(c, "sample-repo")
-	if lf.Type != "commit" || lf.Repo != "sample-repo" {
-		t.Fatalf("leaf meta = %+v", lf)
-	}
-	if lf.Source != "sample-repo@a1b2c3d4e5f6aaaa" {
-		t.Fatalf("source = %s", lf.Source)
-	}
-	if lf.Related != "README.md,src/main.c" {
-		t.Fatalf("related = %s", lf.Related)
-	}
-	if lf.Heading != "commit a1b2c3d4e5f6 — feat: first commit" {
-		t.Fatalf("heading = %q", lf.Heading)
-	}
-	if !strings.Contains(lf.Text, "Ada Lovelace") || !strings.Contains(lf.Text, "README.md") {
-		t.Fatalf("text = %s", lf.Text)
-	}
-}
-
-func TestRepoNameFromOrigin(t *testing.T) {
-	dir := initRepo(t, []commitSpec{{
-		when: time.Now(), name: "Ada Lovelace", email: "ada@example.com",
-		subject: "init", files: map[string]string{"README.md": "x"},
-	}})
-	r, err := git.PlainOpen(dir)
-	if err != nil {
-		t.Fatal(err)
-	}
-	if _, err := r.CreateRemote(&config.RemoteConfig{
-		Name: "origin",
-		URLs: []string{"https://git.example.com/eSlider/sample-repo.git"},
-	}); err != nil {
-		t.Fatal(err)
-	}
-	name, err := RepoName(dir)
-	if err != nil {
-		t.Fatal(err)
-	}
-	if name != "sample-repo" {
-		t.Fatalf("RepoName = %q, want sample-repo", name)
-	}
-}
-
-func TestRepoNameFallsBackToDir(t *testing.T) {
-	dir := initRepo(t, []commitSpec{{
-		when: time.Now(), name: "Ada Lovelace", email: "ada@example.com",
-		subject: "init", files: map[string]string{"README.md": "x"},
-	}})
-	name, err := RepoName(dir)
-	if err != nil {
-		t.Fatal(err)
-	}
-	if name != filepath.Base(dir) {
-		t.Fatalf("RepoName = %q, want %s", name, filepath.Base(dir))
-	}
-}
-
-type commitSpec struct {
-	when    time.Time
-	name    string
-	email   string
-	subject string
-	files   map[string]string
-}
-
-func initRepo(t *testing.T, specs []commitSpec) string {
-	t.Helper()
-	dir := t.TempDir()
-	r, err := git.PlainInit(dir, false)
-	if err != nil {
-		t.Fatal(err)
-	}
-	w, err := r.Worktree()
-	if err != nil {
-		t.Fatal(err)
-	}
-	for _, s := range specs {
-		for path, body := range s.files {
-			full := filepath.Join(dir, path)
-			if err := os.MkdirAll(filepath.Dir(full), 0o755); err != nil && !os.IsExist(err) {
-				t.Fatal(err)
-			}
-			if err := os.WriteFile(full, []byte(body), 0o644); err != nil {
-				t.Fatal(err)
-			}
-			if _, err := w.Add(path); err != nil {
-				t.Fatal(err)
-			}
-		}
-		if _, err := w.Commit(s.subject, &git.CommitOptions{
-			Author: &object.Signature{Name: s.name, Email: s.email, When: s.when},
-		}); err != nil {
-			t.Fatal(err)
-		}
-	}
-	return dir
-}
-
-func subjects(cs []Commit) []string {
-	out := make([]string, len(cs))
-	for i, c := range cs {
-		out[i] = c.Subject
-	}
-	return out
-}

internal/httpapi/server.go

@@ -1,10 +1,10 @@
-// Package httpapi serves the 2dph brain over HTTP.
+// Package server serves the 2dph brain over HTTP.
 //
 // Async by design: every request runs on its own goroutine, and CPU-heavy
-// searches are serialized through a bounded worker pool so N requests can't
-// spawn N backends at once.
+// searches are serialized through a bounded worker pool (a counting
+// semaphore) so N requests can't spawn N search processes at once.
 //
-// Used by bin/brain/serve.go. Tests inject a fake API (no exec, no ladybug).
+// Used by bin/brain/serve.go.
 package httpapi
 
 import (
@@ -21,45 +21,30 @@ import (
 	"time"
 )
 
-// API is the in-process brain surface. Production serve.go wires internal/brain.
-type API interface {
+type Searcher interface {
 	Search(ctx context.Context, query string, limit int) ([]byte, error)
-	Get(ctx context.Context, id string, body bool) ([]byte, error)
-	Stats(ctx context.Context) ([]byte, error)
-	Audit(ctx context.Context) ([]byte, error)
-	Ingest(ctx context.Context) ([]byte, error)
 }
 
 type Server struct {
-	api       API
+	searcher  Searcher
 	semaphore chan struct{}
 }
 
 const defaultPort = 8630
 
-var errUnimplemented = errors.New("not implemented")
-
-func NewServer(api API, workers int) http.Handler {
+func NewServer(searcher Searcher, workers int) http.Handler {
 	return &Server{
-		api:       api,
+		searcher:  searcher,
 		semaphore: make(chan struct{}, workers),
 	}
 }
 
 func (s *Server) ServeHTTP(w http.ResponseWriter, r *http.Request) {
-	switch r.URL.Path {
-	case "/health":
+	switch {
+	case r.URL.Path == "/health":
 		writeJSON(w, http.StatusOK, map[string]any{"status": "ok"})
-	case "/search":
+	case r.URL.Path == "/search":
 		s.handleSearch(w, r)
-	case "/get":
-		s.handleGet(w, r)
-	case "/stats":
-		s.handleJSON(w, r, s.api.Stats)
-	case "/audit":
-		s.handleJSON(w, r, s.api.Audit)
-	case "/ingest":
-		s.handleJSON(w, r, s.api.Ingest)
 	default:
 		writeJSON(w, http.StatusNotFound, map[string]any{"error": "not found"})
 	}
@@ -80,56 +65,19 @@ func (s *Server) handleSearch(w http.ResponseWriter, r *http.Request) {
 		}
 		limit = n
 	}
-	if !s.acquire(w, r) {
-		return
-	}
-	defer s.release()
-	body, err := s.api.Search(r.Context(), q, limit)
-	writeAPI(w, body, err)
-}
 
-func (s *Server) handleGet(w http.ResponseWriter, r *http.Request) {
-	id := strings.TrimSpace(r.URL.Query().Get("id"))
-	if id == "" {
-		writeJSON(w, http.StatusBadRequest, map[string]any{"error": "id required"})
-		return
-	}
-	body := r.URL.Query().Get("body") == "1" || r.URL.Query().Get("body") == "true"
-	if !s.acquire(w, r) {
-		return
-	}
-	defer s.release()
-	out, err := s.api.Get(r.Context(), id, body)
-	writeAPI(w, out, err)
-}
-
-func (s *Server) handleJSON(w http.ResponseWriter, r *http.Request, fn func(context.Context) ([]byte, error)) {
-	if !s.acquire(w, r) {
-		return
-	}
-	defer s.release()
-	body, err := fn(r.Context())
-	writeAPI(w, body, err)
-}
-
-func (s *Server) acquire(w http.ResponseWriter, r *http.Request) bool {
+	// Worker pool: block until a slot frees, so burst concurrency still
+	// bounds memory (no unbounded python processes).
 	select {
 	case s.semaphore <- struct{}{}:
-		return true
+		defer func() { <-s.semaphore }()
 	case <-r.Context().Done():
-		return false
-	}
+		return
 	}
 
-func (s *Server) release() { <-s.semaphore }
-
-func writeAPI(w http.ResponseWriter, body []byte, err error) {
+	body, err := s.searcher.Search(r.Context(), q, limit)
 	if err != nil {
-		code := http.StatusBadGateway
-		if errors.Is(err, errUnimplemented) {
-			code = http.StatusNotImplemented
-		}
-		writeJSON(w, code, map[string]any{"error": err.Error()})
+		writeJSON(w, http.StatusGatewayTimeout, map[string]any{"error": err.Error()})
 		return
 	}
 	writeRaw(w, http.StatusOK, body)
@@ -147,20 +95,17 @@ func writeRaw(w http.ResponseWriter, code int, body []byte) {
 	w.Write(body)
 }
 
-// ExecSearcher shells out to var/bin/brain-search. Fallback when the serve
-// binary is built without ladybug cgo (CI / tags=brain_serve only).
-type ExecSearcher struct {
-	CmdPath string
-	Timeout time.Duration
+// brainSearcher shells out to the Go brain-search binary (not Python).
+// A single search is bounded and short-lived; the worker pool keeps at most N live.
+type brainSearcher struct {
+	cmdPath string
+	timeout time.Duration
 }
 
-func (b ExecSearcher) Search(ctx context.Context, query string, limit int) ([]byte, error) {
-	if b.Timeout == 0 {
-		b.Timeout = 60 * time.Second
-	}
-	ctx, cancel := context.WithTimeout(ctx, b.Timeout)
+func (b *brainSearcher) Search(ctx context.Context, query string, limit int) ([]byte, error) {
+	ctx, cancel := context.WithTimeout(ctx, b.timeout)
 	defer cancel()
-	cmd := exec.CommandContext(ctx, b.CmdPath, "--json", "-n", strconv.Itoa(limit), query)
+	cmd := exec.CommandContext(ctx, b.cmdPath, "--json", "-n", strconv.Itoa(limit), query)
 	out, err := cmd.Output()
 	if err != nil {
 		var exitErr *exec.ExitError
@@ -172,18 +117,6 @@ func (b ExecSearcher) Search(ctx context.Context, query string, limit int) ([]by
 	return out, nil
 }
 
-func (ExecSearcher) Get(context.Context, string, bool) ([]byte, error) {
-	return nil, errUnimplemented
-}
-func (ExecSearcher) Stats(context.Context) ([]byte, error) { return nil, errUnimplemented }
-func (ExecSearcher) Audit(context.Context) ([]byte, error) { return nil, errUnimplemented }
-func (ExecSearcher) Ingest(context.Context) ([]byte, error) {
-	return json.Marshal(map[string]any{
-		"mode":    "rebuild",
-		"command": "bin/brain/index.go --rebuild",
-	})
-}
-
 func defaultSearchCmd(root string) string {
 	if env := os.Getenv("KB_SEARCH_CMD"); env != "" {
 		return env
@@ -191,7 +124,11 @@ func defaultSearchCmd(root string) string {
 	return filepath.Join(root, "var", "bin", "brain-search")
 }
 
-func workersAndPort() (int, int) {
+// Run starts the HTTP server. Reads env: KB_SEARCH_CMD (default
+// $KB_ROOT/var/bin/brain-search), KB_WORKERS (default 4), KB_PORT (default 8630).
+func Run() {
+	root := os.Getenv("KB_ROOT")
+	searchPath := defaultSearchCmd(root)
 	workers := 4
 	if raw := os.Getenv("KB_WORKERS"); raw != "" {
 		if n, err := strconv.Atoi(raw); err == nil && n > 0 {
@@ -204,19 +141,11 @@ func workersAndPort() (int, int) {
 			port = n
 		}
 	}
-	return workers, port
-}
 
-// Run starts the HTTP server with an injected API (in-process brain, or ExecSearcher).
-func Run(api API) {
-	if api == nil {
-		root := os.Getenv("KB_ROOT")
-		api = ExecSearcher{CmdPath: defaultSearchCmd(root), Timeout: 60 * time.Second}
-	}
-	workers, port := workersAndPort()
-	handler := NewServer(api, workers)
+	searcher := &brainSearcher{cmdPath: searchPath, timeout: 60 * time.Second}
+	handler := NewServer(searcher, workers)
 	addr := "127.0.0.1:" + strconv.Itoa(port)
-	log.Printf("serve: %s (workers=%d)", addr, workers)
+	log.Printf("serve: %s (workers=%d cmd=%s)", addr, workers, searchPath)
 	if err := http.ListenAndServe(addr, handler); err != nil {
 		log.Fatal(err)
 	}

internal/httpapi/server_test.go

@@ -5,7 +5,6 @@ import (
 	"encoding/json"
 	"net/http"
 	"net/http/httptest"
-	"os"
 	"strings"
 	"sync"
 	"sync/atomic"
@@ -48,26 +47,6 @@ func (f *fakeSearcher) Search(ctx context.Context, query string, limit int) ([]b
 	return []byte(`{"query":"` + query + `","count":0,"results":[]}`), nil
 }
 
-func (f *fakeSearcher) Get(_ context.Context, id string, body bool) ([]byte, error) {
-	out := map[string]any{"id": id, "root": "info"}
-	if body {
-		out["text"] = "fake body"
-	}
-	return json.Marshal(out)
-}
-
-func (f *fakeSearcher) Stats(context.Context) ([]byte, error) {
-	return []byte(`{"total":0,"by_root":{}}`), nil
-}
-
-func (f *fakeSearcher) Audit(context.Context) ([]byte, error) {
-	return []byte(`{"status":"ok"}`), nil
-}
-
-func (f *fakeSearcher) Ingest(context.Context) ([]byte, error) {
-	return []byte(`{"mode":"rebuild","command":"bin/brain/index.go --rebuild"}`), nil
-}
-
 func (f *fakeSearcher) count() int {
 	f.mu.Lock()
 	defer f.mu.Unlock()
@@ -163,47 +142,6 @@ func TestSearchRejectsBadLimit(t *testing.T) {
 	}
 }
 
-func TestGetLeaf(t *testing.T) {
-	fs := &fakeSearcher{callback: func(q string, limit int) ([]byte, error) {
-		return []byte(`{}`), nil
-	}}
-	h := NewServer(fs, 1)
-	if code, _ := get(t, h, "/get"); code != http.StatusBadRequest {
-		t.Fatalf("missing id code = %d, want 400", code)
-	}
-	code, body := get(t, h, "/get?id=leaf-1&body=1")
-	if code != http.StatusOK {
-		t.Fatalf("get code = %d, want 200 body=%s", code, body)
-	}
-	if !strings.Contains(string(body), "leaf-1") {
-		t.Fatalf("get body %s missing id", body)
-	}
-}
-
-func TestStatsAuditIngest(t *testing.T) {
-	h := NewServer(&fakeSearcher{}, 1)
-	for _, path := range []string{"/stats", "/audit", "/ingest"} {
-		code, body := get(t, h, path)
-		if code != http.StatusOK {
-			t.Fatalf("%s code = %d, want 200 (%s)", path, code, body)
-		}
-		if !json.Valid(body) {
-			t.Fatalf("%s body not json: %s", path, body)
-		}
-	}
-}
-
-func TestHTTPPackageDoesNotExecPython(t *testing.T) {
-	raw, err := os.ReadFile("server.go")
-	if err != nil {
-		t.Fatal(err)
-	}
-	lower := strings.ToLower(string(raw))
-	if strings.Contains(lower, "python3") || strings.Contains(lower, "bin/kb/search") {
-		t.Fatal("httpapi must not exec Python or bin/kb/search")
-	}
-}
-
 func TestDefaultSearchCmdIsBrainNotPython(t *testing.T) {
 	t.Setenv("KB_SEARCH_CMD", "")
 	cmd := defaultSearchCmd("/repo")

skills/agent-cost/SKILL.md

@@ -0,0 +1,34 @@
+---
+name: agent-cost
+description: >-
+  Measure what an agent session actually costs in tokens using bin/agents/cost.
+  Use before and after changing documentation, skills or context layout, and when
+  a session feels unexpectedly expensive.
+---
+
+# agent-cost
+
+```bash
+bin/agents/cost                        # every project, YAML
+bin/agents/cost --repo 2dph            # only sessions whose cwd matches
+bin/agents/cost --json | jq .cursor.by_tool
+bin/agents/cost --snapshot after-x --repo 2dph   # append a row to docs/CONTEXT-BUDGET.md
+```
+
+Reads local session storage from OpenCode and Cursor transcripts. Reports the
+always-loaded baseline, cache hit/miss/thrash, and which tools moved the most
+bytes.
+
+## How to read it
+
+- **Baseline** is what every single message pays for: `AGENTS.md` plus anything
+  eagerly linked from it. Keep it small; it multiplies by message count.
+- **Cache thrash** matters more than raw size. Editing a file that sits early in
+  the context invalidates the prompt cache for the whole session.
+- **by_tool bytes** shows where the real spend is. Usually it is unfiltered
+  command output, not documentation.
+
+## Rule
+
+Measure before and after. A claim that something "reduces tokens" without a
+before and an after number is an opinion, not a result.

skills/diataxis-docs/SKILL.md

@@ -30,7 +30,7 @@ related:
 ---
 ```
 
-`bin/brain/index.go` reads this. `type` becomes a searchable column. `related:` is
+`bin/kb/index` reads this. `type` becomes a searchable column. `related:` is
 frontmatter for humans; graph hops from it are not implemented yet.
 
 ```bash

skills/kb-search/SKILL.md

@@ -1,5 +1,5 @@
 ---
-name: brain
+name: kb-search
 description: >-
   Deduction search over the 2dph brain (Ladybug graph: ops corpus, portfolio,
   ssh hosts) with bin/brain/search.go instead of reading files or grepping
@@ -8,7 +8,7 @@ description: >-
   documentation.
 ---
 
-# brain — deduction over facts and info
+# kb-search — deduction over facts and info
 
 One embedded Ladybug graph (`var/kb.lbug`, read-only when queried) holding two
 roots:
@@ -26,9 +26,9 @@ second independent source when local roots cannot confirm. An answer is
 bin/brain/search.go "Matrix federation"                # pointers + snippets, YAML
 bin/brain/search.go "onlyoffice postgres" --root facts # restrict to confirmed
 bin/brain/search.go "where is cs-lexicon" --json | yq '.[].ref'
-bin/brain/get.go <id> --body                           # full chunk only when needed
-bin/brain/stats.go                                     # index health
-bin/brain/eval.go                                      # recall@5 >= 0.95 gate
+bin/kb/get <id> --body                                 # full chunk only when needed
+bin/kb/stats                                           # index health
+bin/kb/eval                                            # recall@5 >= 0.95 gate
 ```
 
 `bin/kb/search` is a deprecated wrapper. `--hop` errors (File/FROM_FILE edges
@@ -39,7 +39,7 @@ are not wired yet); do not treat it as a graph walk.
 - Search before you read. Never grep a repo for a concept the graph covers.
 - `--root facts` returns only confirmed evidence-linked answers. Default shows
   facts first, then info leafs clearly marked `(not confirmed)`.
-- If recall looks wrong, run `bin/brain/eval.go`; it gates control questions and
+- If recall looks wrong, run `bin/kb/eval`; it gates control questions and
   should stay at or above 95% recall@5.
 - Escalate to `web-search` (the `web-search` skill) as the independent second
   source when both local roots cannot confirm; never report an unconfirmed