feat(httpapi): default search backend is var/bin/brain-search.

bin/brain/serve.go is the command; bin/serve.go stays as a tagged
deprecation shim. Tests fail if the default path still names Python.

AGENTS.md

@@ -36,13 +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/brain/    search.go, serve.go; libs in internal/brain and internal/httpapi
-bin/chats/    sync.go import.go facts.go apply.go; libs in internal/chats
+internal/     shared Go (brain/rank is cgo-free)
-bin/mail/     sync.go import.go (index_mail → brain/index.go)
+bin/watch/    corpus watcher (internal via bin/brain/watch later)
-bin/markdown/ import.go (mistune leafs)
+bin/mail/     mail pipeline: sync (Go), import (md), index_mail (rebuild)
-bin/postgres/ query.go (read-only YAML)
-internal/     shared Go (brain/rank is cgo-free; chats parsers too)
-bin/watch/    corpus watcher (used by bin/brain/watch.go)
 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/)
@@ -56,8 +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/mail/import --from-raw var/mail                                     # message.json → message.md (convert only)
-bin/brain/index.go --rebuild                                            # rebuild brain incl. all mail (fresh DB)
+bin/mail/index_mail                                                     # rebuild brain incl. all mail (fresh DB)
 ```
 
 - `sync` (Go) downloads messages + attachments; Gmail uses paginated list +
@@ -66,7 +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
@@ -79,9 +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/postgres/query.go --profile onlyoffice -c 'SELECT 1'
 bin/md/tables                                     # what the graph holds → YAML
 bin/brain/deduce "question"                       # thinking wrapper
 ```

PLAN.md

@@ -26,10 +26,10 @@ detective method: **a fact needs ≥2 independent sources or it is
 |---|----------|--------|
 | D1 | RAG corpus | ops stack (chat, onlyoffice, gitea/NPM, searchxng, observability, ai-bot, mcp-servers, `~/.ssh/config`) + portfolio. Exclude `office.dev` + jobs/applications. |
 | D2 | skill merging | integrate skills **in this project** `skills/`; skip gitea / brain-dependent skills. |
-| 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”. |
+| D3 | web search | import `web-search`, retire local `searxng-ops`. Vendored here, no remote link. |
 | 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`, `internal/brain`); Python remains for index/write until the Go write path is safe. |
+| D6 | graph engine | **LadybugDB** (Kuzu successor, MIT, embedded, native FTS+vector+Cypher). Python binding for `bin/*`; Go shebang for golang tools. |
 | 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. |
@@ -40,8 +40,6 @@ detective method: **a fact needs ≥2 independent sources or it is
 | D14 | tooling style | `bin/{subject}/{method}.go` shebang (e.g. `bin/brain/search.go`). Shared code in `internal/`. One root `go.mod` + `go.work`. No `bin/*/main.go`, no nested modules. |
 | D15 | repo | Gitea [`eSlider/2dph`](https://git.produktor.io/eSlider/2dph) is origin + [issues](https://git.produktor.io/eSlider/2dph/issues). GitHub `eSlider/2dph` is the public clone (PRs + Actions CI). No direct `main` pushes. TDD → PR → CI green → merge. |
 | 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. |
 
 ## Architecture
 
@@ -53,17 +51,10 @@ detective method: **a fact needs ≥2 independent sources or it is
   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)
+    kb/index                build FTS + HNSW from corpus
-    brain/index.go          rebuild FTS + HNSW (incl. --with-mail)
+    kb/search               deduction: facts → info → web-search; --hop N
-    brain/get.go stats.go eval.go watch.go
+    kb/get  kb/stats  kb/eval
-    brain/search.go         deduction: facts → info → web-search
+    md/import  md/select  md/tables  md/gaps     (mistune)
-    brain/serve.go          HTTP API (internal/httpapi)
-    mail/import.go          JSON → markdown (no brain write)
-    markdown/import.go      mistune leaves
-    postgres/query.go       read-only YAML (wraps bin/db/psql-yq)
-    chats/sync.go import.go facts.go apply.go
-                            (libs in internal/chats; no chats index)
-    md/import               (deprecated; bin/markdown/import.go)
     brain/extract  brain/audit   brain/deduce    (thinking wrapper)
     web/search               (vendored)
     db/psql-yq               (vendored)
@@ -112,26 +103,26 @@ 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
+   indexing stay separate for crash safety.
-   deprecation shim.
 4. Result: 17,835 messages → 28,918 info leafs, FTS + HNSW healthy, searchable
-   via `bin/brain/search.go`.
+   via `bin/kb/search`.
 
 ## CI/CD pipeline (D15)
 
 `.github/workflows/ci.yml`:
 
-1. go vet + go test ./... (root module; packages without ladybug cgo)
+1. go vet + go test ./... (Go tools; root module)
-2. `go test ./internal/brain/rank` (cgo-free ranking + flag parser)
+2. `go test ./rank` in `bin/kbsearch` (cgo-free ranking + flag parser; nested module still needs ladybug for the rest)
-3. python -m unittest discover -s bin/tools (includes published-docs SoT)
+3. `go test ./...` in `bin/chats` (Telegram + LinkedIn parsers; nested module)
-4. bin/facts/audit self  (lexicon internal consistency)
+4. python -m unittest discover (Py tools)
-5. bin/brain/eval.go       (recall@5 ≥ 0.95, gates index regressions)
+5. bin/facts/audit self  (lexicon internal consistency)
-6. md-docs build/lint if docs tooling arrives.
+6. bin/kb/eval            (recall@5 ≥ 0.95, gates index regressions)
+7. md-docs build/lint if docs tooling arrives.
 
 Feedback loop: every commit → PR → CI → green/gate → merge. Same discipline as
 `db/tech-poc`: contract first where there is an OpenAPI/message shape.

README.md

@@ -30,9 +30,9 @@ 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"]
+        IDX["bin/kb/index<br/>chunk + embed"]
-        MD["bin/markdown/import.go<br/>mistune leaves"]
+        MD["bin/md/import<br/>mistune leaves"]
-        SR["bin/brain/search.go<br/>deduction"]
+        SR["bin/kb/search<br/>deduction + --hop"]
     end
 
     subgraph store["Ladybug var/kb.lbug"]
@@ -85,23 +85,21 @@ fact; conflicting sources or a single source → `hypothesis` → `(not confirme
 ## Deduction search
 
 ```bash
-bin/brain/search.go "Matrix federation over HTTPS"   # facts → info → web-search
+bin/kb/search "Matrix federation over HTTPS"      # facts → info → web-search
-bin/brain/search.go "onlyoffice postgres" --root facts
+bin/kb/search "what runs on arc-2" --hop 1        # walk graph edges
-bin/brain/search.go "where is cs-lexicon" --json | yq '.'
+bin/kb/search "where is cs-lexicon" --json | yq '.'  # YAML by default
-bin/brain/get.go <id> --body                         # full chunk on demand
+bin/kb/get <id> --body                            # full chunk on demand
-bin/brain/stats.go                                   # index health
+bin/kb/stats                                      # index health
-bin/brain/eval.go                                    # recall@5 gate
+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`.
-
 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/mail/import --from-raw var/mail                                     # JSON → markdown
-bin/brain/index.go --rebuild                                            # rebuild brain (incl. mail)
+bin/mail/index_mail                                                     # rebuild brain incl. mail
-bin/brain/search.go "invoice from last week"                            # same search over mail leafs
+bin/kb/search "Mietwagen Nürnberg invoice"                              # now answers from mail
 ```
 
 ## Storage
@@ -111,7 +109,7 @@ 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
@@ -119,10 +117,10 @@ bin/brain/search.go "invoice from last week"                            # same s
 
 ## Tooling conventions
 
-`bin/{subject}/{method}.go` — self-describing: shebang on line 1, usage comment
+`bin/{subject}/{method}` — self-describing: shebang on line 1, usage comment
-from line 2. Shared code in `internal/`. YAML default output, `--json` for
+from line 2. bash + python primary; golang via the Go shebang when a compiled
-machines. Tests gate every commit. HTTP: `bin/brain/serve.go` (default search
+helper is right. YAML default output, `--json` for machines. Everything that
-binary `var/bin/brain-search`, not Python).
+touches network/db is read-only, throttled, cached. Tests gate every commit.
 
 ## Development
 
@@ -138,7 +136,7 @@ Docker (optional, cached model + var volumes):
 ```bash
 docker compose run --rm brain index            # (re)index corpus
 docker compose run --rm brain search "query"   # one-shot query
-docker compose run --rm brain serve            # bin/brain/serve.go
+docker compose run --rm brain serve            # async Go HTTP server
 docker compose up brain-watch                  # auto re-index on change
 ```
 

bin/brain/doc.go

@@ -1,3 +1,3 @@
-// Commands in this directory are shebang mains (search.go, serve.go, index.go,
+// Commands in this directory are shebang mains (search.go).
-// get.go, stats.go, eval.go, watch.go), each behind an exclusive build tag.
+// 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/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
+func writeFactsToBrain(root string, facts []ExtractedFact) {
-// bin/brain/index.go (not this subject).
+	indexScript := filepath.Join(root, "bin", "kb", "index")
-func writeFactsMarkdown(facts []ExtractedFact) {
+	if _, err := os.Stat(indexScript); os.IsNotExist(err) {
-	mdDir := filepath.Join(Dir(), "facts")
+		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 search <q>      bin/kb/search
-#   brain index           bin/kb/index --with-mail
+#   brain index           bin/kb/index
-#   brain watch <dir>     compiled /app/bin/watch (bin/brain/watch.go)
+#   brain watch <dir>     watchdog re-indexer (bin/kb/watch)
-#   brain serve           compiled /app/bin/serve (bin/brain/serve.go)
+#   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/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
+Indexing is a separate step (bin/mail/index_mail): conversion can crash in
-crash in native docling and must not leave the brain DB mid-transaction.
+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
+Ladybug corrupts its WAL when brand-new leafs are bulk-inserted while the
-shim always rebuilds (repo corpus + var/mail). Conversion stays in mail/import.
+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(
+    p = argparse.ArgumentParser(description="rebuild the brain incl. all mail")
-        "bin/mail/index_mail is deprecated; use bin/brain/index.go --rebuild --with-mail",
+    p.add_argument("--dry-run", action="store_true", help="count only, write nothing")
-        file=sys.stderr,
+    p.add_argument("--limit", type=int, default=0, help="cap messages included")
-    )
+    p.add_argument("--since", default="", help="only messages dated >= YYYY-MM-DD")
-    index = ROOT / "bin" / "kb" / "index"
+    p.add_argument("--json", action="store_true")
-    os.execv(sys.executable, [sys.executable, str(index), "--rebuild", "--with-mail", *argv])
+    a = p.parse_args(argv)
-    return 1
+
+    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/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

@@ -34,60 +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")

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

@@ -1,57 +0,0 @@
-"""Published docs must match live commands (Gitea SoT, brain/search, no fake --hop)."""
-from __future__ import annotations
-
-import re
-import unittest
-from pathlib import Path
-
-ROOT = Path(__file__).resolve().parents[2]
-
-
-class PublishedDocsTest(unittest.TestCase):
-    def test_readme_points_issues_at_gitea(self) -> None:
-        text = (ROOT / "README.md").read_text()
-        self.assertIn(
-            "https://git.produktor.io/eSlider/2dph/issues",
-            text,
-            "README must point issues at Gitea",
-        )
-
-    def test_plan_d15_names_gitea_origin(self) -> None:
-        text = (ROOT / "PLAN.md").read_text()
-        self.assertIn("D15", text)
-        self.assertIn("git.produktor.io/eSlider/2dph", text)
-
-    def test_readme_primary_search_is_brain(self) -> None:
-        text = (ROOT / "README.md").read_text()
-        self.assertIn(
-            "bin/brain/search.go",
-            text,
-            "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_docs_do_not_claim_hop_walks(self) -> None:
-        paths = [
-            ROOT / "README.md",
-            ROOT / "docs" / "design.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.
-        # Honest "not implemented" notes must not match.
-        lie = re.compile(r"--hop (?:N|1).*(?:follow|walk)", re.I | re.S)
-        for path in paths:
-            text = path.read_text()
-            self.assertIsNone(
-                lie.search(text),
-                f"{path.relative_to(ROOT)} still claims --hop walks the graph",
-            )

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
+	// IndexCmd is the kb/index command template. %s is replaced by the repo
-	// root (from KB_ROOT). Defaults to `python3 <root>/bin/kb/index --with-mail`.
+	// 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") {
+	if opts.IndexCmd == "" {
-		t.Fatalf("default index cmd = %q, want kb/index", opts.IndexCmd)
+		t.Fatal("default index cmd is empty")
-	}
-	if !strings.Contains(opts.IndexCmd, "--with-mail") {
-		t.Fatalf("default index cmd must include --with-mail, got %q", opts.IndexCmd)
 	}
 }

docs/README.md

@@ -8,7 +8,4 @@ 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`). `--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/chat sync telegram --limit 100
-./bin/chats/import.go
+./bin/chat import
-./bin/chats/facts.go
+./bin/chat index
-./bin/chats/apply.go --dry-run
+./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

@@ -0,0 +1,33 @@
+# 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

@@ -17,14 +17,14 @@ as one consistent state.
 ## Deduction search
 
 ```
-bin/brain/search.go "question"
+bin/kb/search "question"
   1. facts root   — confirmed answers only   → return with evidence links
   2. info  root   — supporting narrative     → snippets, marked (not confirmed)
   3. web-search   — second independent source → upgrade hypothesis to confirmed
 ```
 
-`--hop` is not implemented yet (needs File/FROM_FILE edges). The flag is an
+`--hop N` follows graph edges (sibling leaves under a heading, owning file,
-error; it is not a graph walk.
+`related:` files, vector-neighbour leaves) — the deduction walk.
 
 ## Who / What / How / Where / When + evidence
 

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)
-	}
-}

skills/diataxis-docs/SKILL.md

@@ -30,11 +30,12 @@ related:
 ---
 ```
 
-`bin/brain/index.go` reads this. `type` becomes a searchable column. `related:` is
+`bin/kb/index` reads this. `type` becomes a searchable column and `related`
-frontmatter for humans; graph hops from it are not implemented yet.
+becomes a graph edge:
 
 ```bash
-bin/brain/search.go "deploy"
+bin/kb/search "deploy" --type howto
+bin/kb/search "Stecktafel" --hop 1     # follow links and related
 ```
 
 ## Audit checklist
@@ -45,7 +46,8 @@ bin/brain/search.go "deploy"
    The indexer chunks on H2, so split files also search better.
 3. Is `status: archive` set on anything superseded? Archived files stay indexed
    but stop competing with current ones for a reader's attention.
-4. Does every explanation link the reference it explains, and vice versa?
+4. Does every explanation link the reference it explains, and vice versa? That
+   link is what `--hop 1` walks.
 
 ## Rule
 

skills/kb-search/SKILL.md

@@ -2,10 +2,9 @@
 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
+  ssh hosts) with bin/kb/search instead of reading files or grepping repos.
-  repos. Use whenever a question starts with "where is", "what runs on",
+  Use whenever a question starts with "where is", "what runs on", "which file
-  "which file describes", "who is", "how is X done", before opening any
+  describes", "who is", "how is X done", before opening any documentation.
-  documentation.
 ---
 
 # kb-search — deduction over facts and info
@@ -23,24 +22,24 @@ second independent source when local roots cannot confirm. An answer is
 `(not confirmed)`.
 
 ```bash
-bin/brain/search.go "Matrix federation"                # pointers + snippets, YAML
+bin/kb/search "Matrix federation"                # pointers + snippets, YAML
-bin/brain/search.go "onlyoffice postgres" --root facts # restrict to confirmed
+bin/kb/search "what runs on arc-2" --hop 1       # follow graph edges
-bin/brain/search.go "where is cs-lexicon" --json | yq '.[].ref'
+bin/kb/search "onlyoffice postgres" --root facts # restrict to confirmed
-bin/brain/get.go <id> --body                           # full chunk only when needed
+bin/kb/search "where is cs-lexicon" --json | yq '.[].ref'
-bin/brain/stats.go                                     # index health
+bin/kb/get <id> --body                           # full chunk only when needed
-bin/brain/eval.go                                      # recall@5 >= 0.95 gate
+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
-are not wired yet); do not treat it as a graph walk.
-
 ## Rules
 
 - 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.
+- `--hop N` follows sibling leaves, owning files, `related:` links and
+  vector-neighbours — that is the deduction walk, not random expansion.
 - Escalate to `web-search` (the `web-search` skill) as the independent second
   source when both local roots cannot confirm; never report an unconfirmed
   single-source local answer as fact.

skills/web-search/SKILL.md

@@ -18,10 +18,9 @@ bin/web/search "postgres partial index" --lang en --fresh year
 
 ## Web or knowledge base
 
-`bin/brain/search.go` holds our own facts: the ops stack, portfolio, ssh hosts,
+`bin/kb/search` holds our own facts: the ops stack, portfolio, ssh hosts, the
-the lexicon. Go there first. Reach for `bin/web/search` when the answer is
+lexicon. Go there first. Reach for `bin/web/search` when the answer is outside
-outside our repos: upstream library behaviour, vendor documentation, public
+our repos: upstream library behaviour, vendor documentation, public standards.
-standards.
 
 Keep the two apart. A finding is stronger when the reader can see that one
 source was ours and one was not.