daftari 1.6.0 → 1.7.1

package/dist/search/index-state.js

@@ -0,0 +1,68 @@
+// Process-wide indexing state.
+//
+// The MCP server opens the stdio transport before running a cold-start reindex
+// so `initialize` / `tools/list` answer immediately. While that background pass
+// runs the server is alive but search and write tools cannot trust the index;
+// they consult this module to decide whether to serve or to reply "still
+// indexing — N/M chunks". A single in-process snapshot is enough because the
+// server is one Node process per vault.
+function freshState() {
+    return {
+        status: "ready",
+        done: 0,
+        total: 0,
+        error: null,
+        startedAt: null,
+        finishedAt: null,
+    };
+}
+let state = freshState();
+export function getIndexStatus() {
+    return { ...state };
+}
+export function markIndexing() {
+    state = {
+        status: "indexing",
+        done: 0,
+        total: 0,
+        error: null,
+        startedAt: new Date().toISOString(),
+        finishedAt: null,
+    };
+}
+export function setIndexProgress(done, total) {
+    if (state.status !== "indexing")
+        return;
+    state = { ...state, done, total };
+}
+export function markIndexReady() {
+    state = {
+        ...state,
+        status: "ready",
+        error: null,
+        finishedAt: new Date().toISOString(),
+    };
+}
+export function markIndexError(message) {
+    state = {
+        ...state,
+        status: "error",
+        error: message,
+        finishedAt: new Date().toISOString(),
+    };
+}
+// Tests load tools without running main(); resetting the singleton between
+// suites keeps cross-test pollution out of the state machine.
+export function resetIndexState() {
+    state = freshState();
+}
+// Formatted message tools return to clients while indexing is in progress.
+// One place so the phrasing is consistent across vault_search, vault_write,
+// vault_reindex, etc.
+export function indexingBusyMessage(snapshot) {
+    if (snapshot.total > 0) {
+        return `vault is still indexing (${snapshot.done}/${snapshot.total} chunks) — try again shortly`;
+    }
+    return `vault is still indexing — try again shortly`;
+}
+//# sourceMappingURL=index-state.js.map

package/dist/search/index-state.js.map

@@ -0,0 +1 @@
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package/dist/search/reindex.d.ts

@@ -1,4 +1,5 @@
 import { type Result } from "../frontmatter/types.js";
+export declare function isIndexFresh(vaultRoot: string): Promise<boolean>;
 export interface ReindexResult {
     documentCount: number;
     chunkCount: number;

package/dist/search/reindex.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reindex.d.ts","sourceRoot":"","sources":["../../src/search/reindex.ts"],"names":[],"mappings":"AAYA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAgB/D,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IACvB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,cAAc;IAI7B,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,CAAC;CACpD;AA4FD,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,KAAK,CAAC,CAAC,CAsCvC;AAED,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;CACxB;AAQD,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CAmD7C"}
+{"version":3,"file":"reindex.d.ts","sourceRoot":"","sources":["../../src/search/reindex.ts"],"names":[],"mappings":"AAaA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAyE/D,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CActE;AAED,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IACvB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,cAAc;IAI7B,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,CAAC;CACpD;AA4FD,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,KAAK,CAAC,CAAC,CA0CvC;AAED,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;CACxB;AAQD,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CAqE7C"}

package/dist/search/reindex.js

@@ -8,12 +8,92 @@
 // in fixed-size sub-batches so peak memory stays flat as the vault grows. If
 // the model is unavailable the documents (and their BM25 tokens) still index;
 // only the vector column is left NULL and vectorEnabled is false.
+import { stat } from "node:fs/promises";
 import { parseDocument } from "../frontmatter/parser.js";
 import { err, ok } from "../frontmatter/types.js";
-import { clearIndex, deleteDocument, documentCount, insertChunk, insertDocument, openIndexDb, setMeta, } from "../storage/index-db.js";
+import { clearIndex, deleteDocument, documentCount, getMeta, insertChunk, insertDocument, openIndexDb, setMeta, } from "../storage/index-db.js";
 import { listFiles, readFile, resolveVaultPath } from "../storage/local.js";
 import { tokenize } from "./bm25.js";
 import { chunkText, EMBEDDING_DIM, embed } from "./vector.js";
+// Manifest key in the meta table: JSON object mapping vault-relative path to
+// mtime in ms. Written at the end of a successful reindex and updated by
+// indexDocument after each incremental write, so a startup freshness check
+// can decide whether the persisted index already reflects the files on disk.
+const MANIFEST_META_KEY = "vault_manifest";
+// Walks the vault and produces a fresh path→mtimeMs map. Returns null if any
+// file cannot be stat'd or the file listing fails — caller treats null as
+// "can't prove freshness, fall back to a full reindex."
+async function buildManifest(vaultRoot) {
+    const list = await listFiles(vaultRoot);
+    if (!list.ok)
+        return null;
+    const manifest = {};
+    for (const relPath of list.value) {
+        const resolved = resolveVaultPath(vaultRoot, relPath);
+        if (!resolved.ok)
+            return null;
+        try {
+            const st = await stat(resolved.value);
+            manifest[relPath] = st.mtimeMs;
+        }
+        catch {
+            return null;
+        }
+    }
+    return manifest;
+}
+function readManifest(db) {
+    const raw = getMeta(db, MANIFEST_META_KEY);
+    if (!raw)
+        return null;
+    try {
+        const parsed = JSON.parse(raw);
+        if (!parsed || typeof parsed !== "object" || Array.isArray(parsed))
+            return null;
+        return parsed;
+    }
+    catch {
+        return null;
+    }
+}
+function writeManifest(db, manifest) {
+    setMeta(db, MANIFEST_META_KEY, JSON.stringify(manifest));
+}
+function manifestsMatch(a, b) {
+    const aKeys = Object.keys(a);
+    const bKeys = Object.keys(b);
+    if (aKeys.length !== bKeys.length)
+        return false;
+    for (const key of aKeys) {
+        if (a[key] !== b[key])
+            return false;
+    }
+    return true;
+}
+// Returns true when the persisted index already reflects every markdown file
+// on disk: doc count is non-zero, a manifest exists, and every file's mtime
+// matches the stored value. Used by `main()` to skip a 20+ minute re-embed
+// pass on every restart of a vault that hasn't changed.
+export async function isIndexFresh(vaultRoot) {
+    const dbResult = openIndexDb(vaultRoot);
+    if (!dbResult.ok)
+        return false;
+    const db = dbResult.value;
+    try {
+        if (documentCount(db) === 0)
+            return false;
+        const stored = readManifest(db);
+        if (!stored)
+            return false;
+        const current = await buildManifest(vaultRoot);
+        if (!current)
+            return false;
+        return manifestsMatch(stored, current);
+    }
+    finally {
+        db.close();
+    }
+}
 // Reads and parses a single markdown file into the shape the index needs.
 // Returns null when the file should be skipped (unreadable, or malformed YAML
 // frontmatter) so a reindex never aborts on one bad file.
@@ -115,6 +195,11 @@ export async function reindexVault(vaultRoot, opts = {}) {
         setMeta(db, "indexed_at", indexedAt);
         setMeta(db, "vector_enabled", String(vectorEnabled));
         setMeta(db, "embedding_dim", String(EMBEDDING_DIM));
+        // Persist a freshness manifest so the next startup can skip this whole
+        // pass when nothing on disk has changed.
+        const manifest = await buildManifest(vaultRoot);
+        if (manifest)
+            writeManifest(db, manifest);
         return ok({
             documentCount: staged.length,
             chunkCount,
@@ -180,6 +265,25 @@ export async function indexDocument(vaultRoot, relPath) {
             });
         });
         write();
+        // Keep the freshness manifest in sync with this single write so the next
+        // startup still sees a current index. Stat the file we just indexed and
+        // patch only its entry — re-statting the whole vault would defeat the
+        // point of the incremental path.
+        const stored = readManifest(db);
+        if (stored) {
+            const resolved = resolveVaultPath(vaultRoot, relPath);
+            if (resolved.ok) {
+                try {
+                    const st = await stat(resolved.value);
+                    stored[relPath] = st.mtimeMs;
+                    writeManifest(db, stored);
+                }
+                catch {
+                    // ignore — manifest just stays stale for this entry; worst case is
+                    // one extra reindex on next startup.
+                }
+            }
+        }
         return ok({ chunkCount: chunks.length, vectorEnabled });
     }
     catch (e) {

package/dist/search/reindex.js.map

@@ -1 +1 @@
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package/dist/tools/search.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,KAAK,aAAa,EAAW,MAAM,mBAAmB,CAAC;AAChE,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAEL,KAAK,kBAAkB,EAGvB,KAAK,mBAAmB,EAEzB,MAAM,qBAAqB,CAAC;AAQ7B,OAAO,EAAE,KAAK,aAAa,EAAgB,MAAM,sBAAsB,CAAC;AAExE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAkEhD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CA2B5C;AAMD,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CA2B7C;AAMD,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAahG;AAgBD,eAAO,MAAM,WAAW,EAAE,cAAc,EA2DvC,CAAC"}

package/dist/tools/search.js

@@ -6,22 +6,43 @@
 // it. If the index is empty (first run after a fresh clone) they trigger a
 // reindex first, so search works without an explicit setup step.
 import { canRead } from "../access/rbac.js";
-import { ok } from "../frontmatter/types.js";
+import { err, ok } from "../frontmatter/types.js";
 import { DEFAULT_WEIGHTS, hybridSearch, relatedSearch, } from "../search/hybrid.js";
+import { getIndexStatus, indexingBusyMessage, markIndexError, markIndexing, markIndexReady, } from "../search/index-state.js";
 import { reindexVault } from "../search/reindex.js";
 import { documentCount, openIndexDb } from "../storage/index-db.js";
-// Builds the index if it has never been built. A populated index is left as-is
-// — callers wanting a refresh use vault_reindex explicitly.
-async function ensureIndexed(vaultRoot) {
+// Gate every index-backed tool on the current indexing state.
+//
+// - "indexing": refuse with a progress-bearing message. The server is still
+//   embedding the vault from cold; the client should retry shortly.
+// - "error":    refuse with the prior failure so the client sees a real
+//   diagnostic instead of an empty / partial result set.
+// - "ready":    fall through to the per-tool logic, with one fallback: if
+//   the SQLite index is empty (a direct test invocation that never went
+//   through main(), or a vault whose .daftari directory was wiped) trigger
+//   a synchronous reindex so search still works without an explicit
+//   --reindex step.
+async function ensureIndexReady(vaultRoot) {
+    const status = getIndexStatus();
+    if (status.status === "indexing") {
+        return err(new Error(indexingBusyMessage(status)));
+    }
+    if (status.status === "error") {
+        return err(new Error(`vault index is in error state: ${status.error ?? "unknown"}`));
+    }
     const dbResult = openIndexDb(vaultRoot);
     if (!dbResult.ok)
         return dbResult;
     const empty = documentCount(dbResult.value) === 0;
     dbResult.value.close();
     if (empty) {
+        markIndexing();
         const reindexed = await reindexVault(vaultRoot);
-        if (!reindexed.ok)
+        if (!reindexed.ok) {
+            markIndexError(reindexed.error.message);
             return reindexed;
+        }
+        markIndexReady();
     }
     return ok(undefined);
 }
@@ -57,7 +78,7 @@ export async function vaultSearch(vaultRoot, args, access) {
             error: new Error("vault_search requires a non-empty 'query' argument"),
         };
     }
-    const ready = await ensureIndexed(vaultRoot);
+    const ready = await ensureIndexReady(vaultRoot);
     if (!ready.ok)
         return ready;
     const dbResult = openIndexDb(vaultRoot);
@@ -90,7 +111,7 @@ export async function vaultSearchRelated(vaultRoot, args, access) {
             error: new Error("vault_search_related requires a non-empty 'path' argument"),
         };
     }
-    const ready = await ensureIndexed(vaultRoot);
+    const ready = await ensureIndexReady(vaultRoot);
     if (!ready.ok)
         return ready;
     const dbResult = openIndexDb(vaultRoot);
@@ -113,9 +134,17 @@ export async function vaultSearchRelated(vaultRoot, args, access) {
     }
 }
 export async function vaultReindex(vaultRoot) {
+    const status = getIndexStatus();
+    if (status.status === "indexing") {
+        return err(new Error(indexingBusyMessage(status)));
+    }
+    markIndexing();
     const result = await reindexVault(vaultRoot);
-    if (!result.ok)
+    if (!result.ok) {
+        markIndexError(result.error.message);
         return result;
+    }
+    markIndexReady();
     return ok({ ...result.value, vault: vaultRoot });
 }
 // ---------------------------------------------------------------------------

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package/dist/tools/write.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"write.d.ts","sourceRoot":"","sources":["../../src/tools/write.ts"],"names":[],"mappings":"AAcA,OAAO,EAAE,KAAK,aAAa,EAAwB,MAAM,mBAAmB,CAAC;AAI7E,OAAO,EAIL,KAAK,WAAW,EAEhB,KAAK,MAAM,EAEX,KAAK,gBAAgB,EACtB,MAAM,yBAAyB,CAAC;AAMjC,OAAO,EAAc,KAAK,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAGtE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAqChD,wBAAgB,sBAAsB,CACpC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC5B,UAAU,EAAE,eAAe,EAAE,GAC5B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CASzB;AAMD,wBAAgB,iBAAiB,CAC/B,EAAE,EAAE,WAAW,EACf,IAAI,EAAE,MAAM,EACZ,UAAU,GAAE,eAAe,EAAO,EAClC,GAAG,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GAChC,MAAM,CAuBR;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,QAAQ,GAAG,QAAQ,GAAG,QAAQ,GAAG,SAAS,GAAG,WAAW,CAAC;IAGjE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,YAAY,EAAE,OAAO,CAAC;CACvB;AAsJD,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAuGrC;AAQD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAyErC;AASD,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAyErC;AASD,wBAAsB,cAAc,CAClC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAqErC;AAuBD,eAAO,MAAM,UAAU,EAAE,cAAc,EAuGtC,CAAC"}
+{"version":3,"file":"write.d.ts","sourceRoot":"","sources":["../../src/tools/write.ts"],"names":[],"mappings":"AAcA,OAAO,EAAE,KAAK,aAAa,EAAwB,MAAM,mBAAmB,CAAC;AAI7E,OAAO,EAIL,KAAK,WAAW,EAEhB,KAAK,MAAM,EAEX,KAAK,gBAAgB,EACtB,MAAM,yBAAyB,CAAC;AAOjC,OAAO,EAAc,KAAK,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAGtE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAqDhD,wBAAgB,sBAAsB,CACpC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC5B,UAAU,EAAE,eAAe,EAAE,GAC5B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CASzB;AAMD,wBAAgB,iBAAiB,CAC/B,EAAE,EAAE,WAAW,EACf,IAAI,EAAE,MAAM,EACZ,UAAU,GAAE,eAAe,EAAO,EAClC,GAAG,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GAChC,MAAM,CAuBR;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,QAAQ,GAAG,QAAQ,GAAG,QAAQ,GAAG,SAAS,GAAG,WAAW,CAAC;IAGjE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,YAAY,EAAE,OAAO,CAAC;CACvB;AAsJD,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAgIrC;AAQD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CA4FrC;AASD,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CA2ErC;AASD,wBAAsB,cAAc,CAClC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC,CAuErC;AAuBD,eAAO,MAAM,UAAU,EAAE,cAAc,EAuGtC,CAAC"}

package/dist/tools/write.js

@@ -16,8 +16,9 @@ import { frontmatterDiff, recordProvenance } from "../curation/provenance.js";
 import { parseDocument } from "../frontmatter/parser.js";
 import { validateFrontmatter } from "../frontmatter/schema.js";
 import { CONFIDENCES, err, ok, } from "../frontmatter/types.js";
-import { loadHooks } from "../hooks/loader.js";
-import { runPreWriteHooks } from "../hooks/runner.js";
+import { loadHooks, loadPreWriteTransformHooks } from "../hooks/loader.js";
+import { runPreWriteHooks, runPreWriteTransformHooks } from "../hooks/runner.js";
+import { getIndexStatus, indexingBusyMessage } from "../search/index-state.js";
 import { indexDocument } from "../search/reindex.js";
 import { readFile, resolveVaultPath } from "../storage/local.js";
 import { loadConfig } from "../utils/config.js";
@@ -29,6 +30,21 @@ import { sha256Hex } from "../utils/hash.js";
 function todayISO() {
     return new Date().toISOString().slice(0, 10);
 }
+// Refuses writes while the index is being (re)built. The write path ends in
+// indexDocument(), which races with a concurrent reindexVault() — the reindex
+// clears the index and re-inserts every document, so a write that lands in
+// between can be wiped or land against a half-built index. Failing fast keeps
+// hooks, locks, and git commits from running for a write we can't index yet.
+function requireIndexReady() {
+    const status = getIndexStatus();
+    if (status.status === "indexing") {
+        return err(new Error(indexingBusyMessage(status)));
+    }
+    if (status.status === "error") {
+        return err(new Error(`vault index is in error state: ${status.error ?? "unknown"}`));
+    }
+    return ok(undefined);
+}
 // A document's RBAC collection: its frontmatter `collection`, falling back to
 // the top-level directory of its vault-relative path.
 function collectionOf(relPath, fm) {
@@ -208,6 +224,9 @@ function readBaseVersion(args, tool) {
 // the full frontmatter; `updated` and `updated_by` are always stamped by the
 // server, and `created` is preserved from the existing document on an update.
 export async function vaultWrite(vaultRoot, args, access) {
+    const ready = requireIndexReady();
+    if (!ready.ok)
+        return ready;
     const path = requireString(args, "path", "vault_write");
     if (!path.ok)
         return path;
@@ -248,6 +267,7 @@ export async function vaultWrite(vaultRoot, args, access) {
             oldFrontmatter = parsed.value.frontmatter;
     }
     const isUpdate = oldFrontmatter !== null;
+    const hookOperation = isUpdate ? "update" : "create";
     // Config-declared schema extensions participate in validation and
     // serialization. A malformed config fails the write loudly, matching the
     // server's loud-config contract.
@@ -255,6 +275,22 @@ export async function vaultWrite(vaultRoot, args, access) {
     if (!config.ok)
         return config;
     const extensions = config.value.schemaExtensions;
+    // Pre-write transform hooks run BEFORE schema validation, so they can
+    // derive or override built-in frontmatter fields the validator would
+    // otherwise reject. Each returns a Partial<Frontmatter>; the runner merges
+    // them Object.assign-style (shallow, last-writer-wins) and the result is
+    // merged back into rawFrontmatter so validation, hooks, and serialization
+    // all see the transformed values. A transform throw or non-object return
+    // becomes a synthetic blocking issue. The loader fails loud, same as the
+    // pre_write loader.
+    const loadedTransformHooks = await loadPreWriteTransformHooks(vaultRoot, config.value.hooks.preWriteTransform);
+    if (!loadedTransformHooks.ok)
+        return loadedTransformHooks;
+    const transformResult = runPreWriteTransformHooks(loadedTransformHooks.value, rawFrontmatter, {
+        path: path.value,
+        operation: hookOperation,
+    });
+    Object.assign(rawFrontmatter, transformResult.merged);
     const { frontmatter, report } = validateFrontmatter(rawFrontmatter, extensions);
     // Pre-write hooks run after built-in schema validation has filled
     // defaults. Their issues merge into the report and are treated the same
@@ -263,12 +299,15 @@ export async function vaultWrite(vaultRoot, args, access) {
     const loadedHooks = await loadHooks(vaultRoot, config.value.hooks.preWrite);
     if (!loadedHooks.ok)
         return loadedHooks;
-    const hookOperation = isUpdate ? "update" : "create";
     const hookIssues = runPreWriteHooks(loadedHooks.value, rawFrontmatter, {
         path: path.value,
         operation: hookOperation,
     });
-    const mergedIssues = [...report.issues, ...hookIssues];
+    const mergedIssues = [
+        ...transformResult.issues,
+        ...report.issues,
+        ...hookIssues,
+    ];
     const mergedReport = {
         valid: mergedIssues.length === 0,
         issues: mergedIssues,
@@ -305,6 +344,9 @@ export async function vaultWrite(vaultRoot, args, access) {
 // Appends a markdown section to an existing document's body, leaving the
 // frontmatter intact apart from the stamped `updated` / `updated_by` fields.
 export async function vaultAppend(vaultRoot, args, access) {
+    const ready = requireIndexReady();
+    if (!ready.ok)
+        return ready;
     const path = requireString(args, "path", "vault_append");
     if (!path.ok)
         return path;
@@ -345,15 +387,25 @@ export async function vaultAppend(vaultRoot, args, access) {
         updated_by: agent.value,
     };
     const newBody = `${parsed.value.content.replace(/\s+$/, "")}\n\n${section.value.trim()}\n`;
-    // Pre-write hooks see the post-stamp frontmatter (the same shape a
-    // subsequent vault_read would return). Issues block the append, same as
-    // for vault_write.
+    // Pre-write transform hooks run before the pre_write validators; their
+    // Partial<Frontmatter> patch is merged Object.assign-style into the
+    // post-stamp frontmatter so the validators below see the transformed
+    // values. A transform throw or non-object return blocks the append.
+    const loadedTransformHooks = await loadPreWriteTransformHooks(vaultRoot, config.value.hooks.preWriteTransform);
+    if (!loadedTransformHooks.ok)
+        return loadedTransformHooks;
+    const transformResult = runPreWriteTransformHooks(loadedTransformHooks.value, newFrontmatter, { path: path.value, operation: "append" });
+    Object.assign(newFrontmatter, transformResult.merged);
+    // Pre-write hooks see the post-stamp, post-transform frontmatter (the same
+    // shape a subsequent vault_read would return). Issues block the append,
+    // same as for vault_write.
     const loadedHooks = await loadHooks(vaultRoot, config.value.hooks.preWrite);
     if (!loadedHooks.ok)
         return loadedHooks;
     const hookIssues = runPreWriteHooks(loadedHooks.value, newFrontmatter, { path: path.value, operation: "append" });
-    if (hookIssues.length > 0) {
-        const summary = hookIssues.map((i) => `${i.field}: ${i.message}`).join("; ");
+    const appendIssues = [...transformResult.issues, ...hookIssues];
+    if (appendIssues.length > 0) {
+        const summary = appendIssues.map((i) => `${i.field}: ${i.message}`).join("; ");
         return err(new Error(`invalid frontmatter: ${summary}`));
     }
     return performWrite({
@@ -379,6 +431,9 @@ export async function vaultAppend(vaultRoot, args, access) {
 // reachable through this tool, and it refuses unless the document's
 // frontmatter is complete and a confidence level has been explicitly set.
 export async function vaultPromote(vaultRoot, args, access) {
+    const ready = requireIndexReady();
+    if (!ready.ok)
+        return ready;
     const path = requireString(args, "path", "vault_promote");
     if (!path.ok)
         return path;
@@ -452,6 +507,9 @@ export async function vaultPromote(vaultRoot, args, access) {
 // commit message; an optional `superseded_by` points at the document that
 // replaces this one.
 export async function vaultDeprecate(vaultRoot, args, access) {
+    const ready = requireIndexReady();
+    if (!ready.ok)
+        return ready;
     const path = requireString(args, "path", "vault_deprecate");
     if (!path.ok)
         return path;