feat: brain/index.go shebang; mail import is not a brain write (D14). (#12)

Commands live at bin/brain/{index,get,stats,eval,watch}.go and
bin/mail/import.go, bin/markdown/import.go, bin/postgres/query.go.
Python remains the Ladybug write worker. index_mail is a deprecation
shim that rebuilds via --with-mail.

AGENTS.md

@@ -36,11 +36,13 @@ 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; libs in internal/brain and internal/httpapi
+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)
 internal/     shared Go (brain/rank is cgo-free; chats parsers too)
-bin/watch/    corpus watcher (internal via bin/brain/watch later)
-bin/mail/     mail pipeline: sync (Go), import (md), index_mail (rebuild)
+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/)
@@ -54,8 +56,8 @@ 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 --from-raw var/mail                                     # message.json → message.md (convert only)
-bin/mail/index_mail                                                     # rebuild brain incl. all mail (fresh DB)
+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)
 ```
 
 - `sync` (Go) downloads messages + attachments; Gmail uses paginated list +
@@ -64,7 +66,7 @@ bin/mail/index_mail                                                     # 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` always rebuilds from scratch (repo corpus + mail). Ladybug
+- `index_mail` is a deprecation shim for `bin/brain/index.go --rebuild`. 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
@@ -77,6 +79,9 @@ 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

@@ -53,13 +53,17 @@ 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                build FTS + HNSW from corpus (Python, for now)
+    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
     brain/search.go         deduction: facts → info → web-search
-    kb/get  kb/stats  kb/eval
     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  md/select  md/tables  md/gaps     (mistune)
+    md/import               (deprecated; bin/markdown/import.go)
     brain/extract  brain/audit   brain/deduce    (thinking wrapper)
     web/search               (vendored)
     db/psql-yq               (vendored)
@@ -108,12 +112,13 @@ 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 --from-raw` — message.json → message.md; PDFs via
+2. `bin/mail/import.go --from-raw` — message.json → message.md; PDFs via
    `pdftotext -layout` (~15ms) with docling subprocess fallback; ICS sidecars
    Latin-1→UTF-8 normalized.
-3. `bin/mail/index_mail` — fresh rebuild (repo corpus + mail) because ladybug
+3. `bin/brain/index.go --rebuild` — 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.
+   indexing stay separate for crash safety. `bin/mail/index_mail` is a
+   deprecation shim.
 4. Result: 17,835 messages → 28,918 info leafs, FTS + HNSW healthy, searchable
    via `bin/brain/search.go`.
 
@@ -125,7 +130,7 @@ 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/kb/eval            (recall@5 ≥ 0.95, gates index regressions)
+5. bin/brain/eval.go       (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

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/kb/index<br/>chunk + embed"]
-        MD["bin/md/import<br/>mistune leaves"]
+        IDX["bin/brain/index.go<br/>chunk + embed"]
+        MD["bin/markdown/import.go<br/>mistune leaves"]
         SR["bin/brain/search.go<br/>deduction"]
     end
 
@@ -88,9 +88,9 @@ 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/kb/get <id> --body                               # full chunk on demand
-bin/kb/stats                                         # index health
-bin/kb/eval                                          # recall@5 gate
+bin/brain/get.go <id> --body                         # full chunk on demand
+bin/brain/stats.go                                   # index health
+bin/brain/eval.go                                    # 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`.
@@ -99,8 +99,8 @@ 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 --from-raw var/mail                                     # JSON → markdown
-bin/mail/index_mail                                                     # rebuild brain incl. mail
+bin/mail/import.go --from-raw var/mail                                  # JSON → markdown
+bin/brain/index.go --rebuild                                            # rebuild brain (incl. mail)
 bin/brain/search.go "invoice from last week"                            # same search over mail leafs
 ```
 
@@ -111,7 +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/kb/index --rebuild`. Use `ensure_indexes()` after upserts.
+  `bin/brain/index.go --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

bin/brain/doc.go

@@ -1,3 +1,3 @@
-// Commands in this directory are shebang mains (search.go).
-// search.go is behind the system_ladybug build tag (cgo).
+// 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.
 package main

bin/brain/eval.go

@@ -0,0 +1,20 @@
+//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

@@ -0,0 +1,20 @@
+//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

@@ -0,0 +1,24 @@
+//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

@@ -0,0 +1,20 @@
+//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

@@ -0,0 +1,20 @@
+//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/docker-entrypoint

@@ -2,10 +2,10 @@
 # bin/docker-entrypoint - run 2dph tools inside the container.
 #
 #   brain                 shell (default)
-#   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 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 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 "$@" ;;
+  index) exec "$KB_PY" /app/bin/kb/index --with-mail "$@" ;;
   watch) exec /app/bin/watch "$@" ;;
   serve) exec /app/bin/serve "$@" ;;
   extract) exec "$KB_PY" /app/bin/facts/extract "$@" ;;

bin/kb/index

@@ -26,6 +26,7 @@ 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"]
 
@@ -99,6 +100,9 @@ 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",
@@ -109,14 +113,26 @@ 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 - re-index the 2dph brain when corpus files change.
+// bin/kb/watch.go — deprecated. Use bin/brain/watch.go.
 //
 // 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/mail/index_mail): conversion can crash in
-native docling and must not leave the brain DB mid-transaction.
+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.
 
 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

@@ -0,0 +1,20 @@
+//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

@@ -1,135 +1,26 @@
 #!/usr/bin/env python3
-"""mail/index_mail - rebuild the brain with every markdown under var/mail.
+"""mail/index_mail — deprecated. Use bin/brain/index.go --rebuild --with-mail.
 
-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)
+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.
 """
 from __future__ import annotations
 
-import argparse
-import json
+import os
 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:
-    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()
+    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
 
 
 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 --from-raw afterwards to convert everything to markdown.
+// bin/mail/import.go --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

@@ -0,0 +1,3 @@
+// 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

@@ -0,0 +1,20 @@
+//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

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

bin/postgres/query.go

@@ -0,0 +1,20 @@
+//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/kb/index --rebuild`).
+    (`bin/brain/index.go --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/kb/index --rebuild. "
+                "Delete var/kb.lbug and run bin/brain/index.go --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/kb/index --rebuild. "
+                "Delete var/kb.lbug and run bin/brain/index.go --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/kb/index first")
+        raise FileNotFoundError(f"{DB_PATH} missing - run bin/brain/index.go --rebuild first")
     db, conn = connect(read_only=True)
     return db, conn

bin/tools/mailleafs.py

@@ -0,0 +1,37 @@
+"""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

@@ -63,3 +63,31 @@ class BinLayoutTest(unittest.TestCase):
             (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

@@ -0,0 +1,46 @@
+"""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

@@ -30,6 +30,15 @@ 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_docs_do_not_claim_hop_walks(self) -> None:
         paths = [
             ROOT / "README.md",

bin/watch/watch.go

@@ -1,4 +1,4 @@
-// Package watch polls corpus directories for changes and re-runs bin/kb/index.
+// Package watch polls corpus directories for changes and re-runs brain/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 kb/index command template. %s is replaced by the repo
-	// root (from KB_ROOT). Defaults to `python3 <root>/bin/kb/index`.
+	// 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 string
 }
 
@@ -67,7 +67,7 @@ func fromEnv(args []string) Options {
 	if pys == "" {
 		pys = "python3"
 	}
-	opts.IndexCmd = pys + " <root>/bin/kb/index"
+	opts.IndexCmd = pys + " <root>/bin/kb/index --with-mail"
 	return opts
 }
 

bin/watch/watch_test.go

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

internal/cmdbin/exec.go

@@ -0,0 +1,54 @@
+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

@@ -0,0 +1,34 @@
+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

@@ -30,7 +30,7 @@ related:
 ---
 ```
 
-`bin/kb/index` reads this. `type` becomes a searchable column. `related:` is
+`bin/brain/index.go` 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

@@ -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/kb/get <id> --body                                 # full chunk only when needed
-bin/kb/stats                                           # index health
-bin/kb/eval                                            # recall@5 >= 0.95 gate
+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/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/kb/eval`; it gates control questions and
+- If recall looks wrong, run `bin/brain/eval.go`; 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