daftari 1.7.0 → 1.8.0

package/CHANGELOG.md

@@ -7,6 +7,59 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.8.0] - 2026-05-20
+
+### Changed
+
+- **Content-addressed embedding cache** (#38, PR #39). Embeddings are no
+  longer keyed by `(path, chunk_index)` — they now live in a separate
+  `embeddings` table keyed by `(content_hash, model)`, where
+  `content_hash` is the SHA-256 of the chunk's text. `chunks` rows carry
+  a `content_hash` column and join to `embeddings` for the current model.
+  A reindex now hashes every chunk, asks the cache which hashes already
+  have a row, and only embeds the misses — so the cost of a reindex
+  scales with the number of *changed chunks*, not the size of the vault.
+  An edit to one paragraph re-embeds one chunk; a rename re-embeds zero;
+  a paragraph moved verbatim to another file re-embeds zero. The
+  composite primary key on `(content_hash, model)` is intentional: a
+  future model migration can keep both the old and new model's
+  embeddings present under the same hash. After writing chunks, the
+  reindex runs an internal `vault_gc` step that drops embeddings rows
+  whose `content_hash` is no longer referenced by any chunk, so the
+  cache does not accumulate orphans. `index.db` rebuilds cleanly on the
+  schema bump (the index is a derived cache); the first reindex after
+  upgrade is a one-time full embed that populates the cache, and every
+  reindex after that is incremental. This is PR 1 of the #38 unbundle;
+  fs.watch reactive indexing, lazy model load, FTS5, sqlite-vec, and
+  pluggable embedding backends are tracked as separate follow-ups.
+
+## [1.7.1] - 2026-05-19
+
+### Fixed
+
+- **MCP server hang at startup** (#35, PR #36). The server no longer re-embeds
+  the entire vault on every launch and no longer waits for indexing to finish
+  before opening the stdio transport. Three compounding bugs are fixed:
+  (1) `main()` always called `reindexVault` even when `.daftari/index.db`
+  already reflected the files on disk — every restart re-embedded the whole
+  vault (~25 minutes on a 3,500-file vault); now a path→mtime manifest is
+  persisted in the SQLite meta table and compared on startup, so an
+  unchanged vault skips the embedding pass entirely. (2) The
+  `StdioServerTransport` opened only after indexing completed, so MCP
+  clients could not answer `initialize` for the whole duration; the
+  transport now opens first and indexing — when required — runs as a
+  background task. (3) Progress was emitted only on TTY stderr, leaving
+  every real (non-TTY) MCP client with zero output during a cold start;
+  progress now streams on stderr in both TTY (\\r-updated) and pipe (full
+  line every ~5%) modes. A new in-process `IndexState`
+  (`ready`/`indexing`/`error` + progress) gates `vault_search`,
+  `vault_search_related`, `vault_reindex`, `vault_write`, `vault_append`,
+  `vault_promote`, and `vault_deprecate` while indexing — those tools
+  return a progress-bearing busy error so clients can retry. Read tools
+  (`vault_read`, `vault_index`, `vault_status`) are unaffected because
+  they go to the filesystem, not the index. `--reindex` remains the one
+  synchronous mode (rebuild, exit).
+
 ## [1.7.0] - 2026-05-19
 
 ### Added

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAgCA,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CASrE;AAED,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,MAAM,GAAG,IAAI,CAE3D;AAED,wBAAsB,IAAI,CAAC,IAAI,GAAE,MAAM,EAA0B,GAAG,OAAO,CAAC,IAAI,CAAC,CAuFhF"}

package/dist/index.js

@@ -1,16 +1,24 @@
 // Daftari MCP server entry point.
 //
 // Parses `--vault <path>`, verifies the vault directory exists, loads the RBAC
-// config, builds the search index, then serves the tools over stdio under the
-// access identity given by `--user` / `--role`. Diagnostics go to stderr so
-// they never corrupt the stdio JSON-RPC stream on stdout.
+// config, opens the MCP stdio transport, then — if the index isn't already
+// current — runs a reindex in the background. Diagnostics go to stderr so they
+// never corrupt the stdio JSON-RPC stream on stdout.
 //
-// `--reindex` rebuilds the search index and exits without starting the server.
+// The transport opens before indexing on purpose: a cold reindex on a large
+// vault is minutes long, and a client must be able to answer `initialize` and
+// list tools immediately. Tools that depend on the index consult
+// `getIndexStatus()` and reply "still indexing — N/M chunks" until the
+// background pass finishes.
+//
+// `--reindex` is the one synchronous mode: rebuild the index, exit, do not
+// start the server.
 import { resolve } from "node:path";
 import { pathToFileURL } from "node:url";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { GUEST_ROLE, resolveAccess } from "./access/rbac.js";
-import { reindexVault } from "./search/reindex.js";
+import { markIndexError, markIndexing, markIndexReady, setIndexProgress, } from "./search/index-state.js";
+import { isIndexFresh, reindexVault } from "./search/reindex.js";
 import { createServer } from "./server.js";
 import { directoryExists } from "./storage/local.js";
 import { loadConfig } from "./utils/config.js";
@@ -58,41 +66,98 @@ export async function main(argv = process.argv.slice(2)) {
     if (access.role === null && roleName !== GUEST_ROLE) {
         process.stderr.write(`daftari: warning: role '${roleName}' not found in config — running as deny-all guest\n`);
     }
-    // Build (or rebuild) the search index. With --reindex this is the whole job.
-    // On an interactive terminal, report embedding progress on a single line so
-    // a large-vault reindex is not silent; in non-TTY contexts (CI, pipes) the
-    // final summary line below is the only output.
-    let progressShown = false;
-    const reindexed = await reindexVault(vaultRoot, {
-        onProgress: process.stderr.isTTY
-            ? (done, total) => {
-                progressShown = true;
-                process.stderr.write(`\rdaftari: embedding ${done}/${total} chunks`);
-            }
-            : undefined,
-    });
-    if (progressShown)
-        process.stderr.write("\n");
-    if (reindexed.ok) {
-        const r = reindexed.value;
-        process.stderr.write(`daftari: indexed ${r.documentCount} docs, ${r.chunkCount} chunks ` +
-            `(vectors ${r.vectorEnabled ? "on" : "off"})\n`);
-    }
-    else {
-        // A failed index is not fatal: lexical search still works and the search
-        // tools retry indexing lazily on first use.
-        process.stderr.write(`daftari: warning: index build failed: ${reindexed.error.message}\n`);
-    }
-    if (argv.includes("--reindex")) {
-        if (!reindexed.ok)
+    // The persisted index is a derived cache: if every file on disk matches the
+    // manifest written by the last reindex, the on-disk index already reflects
+    // the vault and we can skip the embedding pass entirely (~25 min on a
+    // multi-thousand-file vault). --reindex forces a rebuild even when fresh.
+    const forceReindex = argv.includes("--reindex");
+    // --reindex is the one synchronous mode: rebuild and exit. No transport,
+    // no background work. The IndexState is updated for completeness but no
+    // tool runs against it in this mode.
+    if (forceReindex) {
+        markIndexing();
+        const reindexed = await reindexVault(vaultRoot, makeProgressReporter());
+        if (reindexed.ok) {
+            const r = reindexed.value;
+            markIndexReady();
+            process.stderr.write(`daftari: indexed ${r.documentCount} docs, ${r.chunkCount} chunks ` +
+                `(vectors ${r.vectorEnabled ? "on" : "off"})\n`);
+        }
+        else {
+            markIndexError(reindexed.error.message);
+            process.stderr.write(`daftari: warning: index build failed: ${reindexed.error.message}\n`);
             process.exitCode = 1;
+        }
         return;
     }
+    // Open MCP transport first so the client can answer `initialize` and
+    // `tools/list` immediately. Indexing — if needed — runs as a background
+    // task; tools that depend on the index will respond "still indexing" until
+    // it completes.
     const server = createServer(vaultRoot, access);
     const transport = new StdioServerTransport();
     await server.connect(transport);
     process.stderr.write(`daftari: serving vault at ${vaultRoot} (stdio) — ` +
         `user=${access.user} role=${access.roleName}\n`);
+    const fresh = await isIndexFresh(vaultRoot);
+    if (fresh) {
+        process.stderr.write(`daftari: index is up to date — skipping reindex\n`);
+        markIndexReady();
+        return;
+    }
+    // Background reindex. The promise is intentionally not awaited — main()
+    // returns once the transport is up, and the indexing pass runs to
+    // completion alongside the live server.
+    markIndexing();
+    process.stderr.write(`daftari: starting background reindex…\n`);
+    void runBackgroundReindex(vaultRoot);
+}
+async function runBackgroundReindex(vaultRoot) {
+    try {
+        const reindexed = await reindexVault(vaultRoot, makeProgressReporter());
+        if (reindexed.ok) {
+            const r = reindexed.value;
+            markIndexReady();
+            process.stderr.write(`daftari: indexed ${r.documentCount} docs, ${r.chunkCount} chunks ` +
+                `(vectors ${r.vectorEnabled ? "on" : "off"})\n`);
+        }
+        else {
+            markIndexError(reindexed.error.message);
+            process.stderr.write(`daftari: warning: background index build failed: ${reindexed.error.message}\n`);
+        }
+    }
+    catch (e) {
+        const reason = e instanceof Error ? (e.stack ?? e.message) : String(e);
+        markIndexError(reason);
+        process.stderr.write(`daftari: warning: background indexer crashed: ${reason}\n`);
+    }
+}
+// Builds a ReindexOptions whose onProgress streams to both stderr (for
+// operator visibility) and the in-process IndexState (so tools can return
+// progress to MCP clients). TTY stderr gets a \r-updated single line; piped
+// stderr gets a full line every ~5% so MCP-client logs stay readable instead
+// of going silent for tens of minutes.
+function makeProgressReporter() {
+    const PIPE_STEP = 0.05;
+    let nextPipeMark = 0;
+    return {
+        onProgress: (done, total) => {
+            setIndexProgress(done, total);
+            if (total === 0)
+                return;
+            if (process.stderr.isTTY) {
+                process.stderr.write(`\rdaftari: embedding ${done}/${total} chunks`);
+                if (done === total)
+                    process.stderr.write("\n");
+                return;
+            }
+            const ratio = done / total;
+            if (ratio >= nextPipeMark || done === total) {
+                process.stderr.write(`daftari: embedding ${done}/${total} chunks\n`);
+                nextPipeMark = Math.floor(ratio / PIPE_STEP + 1) * PIPE_STEP;
+            }
+        },
+    };
 }
 // Auto-run only when this module is the process entry point (e.g. `tsx
 // src/index.ts`). When imported (by cli.ts or tests) it stays inert.

package/dist/index.js.map

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package/dist/search/hybrid.js

@@ -11,7 +11,7 @@ import { computeDecay } from "../curation/decay.js";
 import { ok } from "../frontmatter/types.js";
 import { getAllChunks, getAllDocuments, getChunksForPath, getDocument, } from "../storage/index-db.js";
 import { buildBm25, searchBm25, tokenize } from "./bm25.js";
-import { cosineSimilarity, embedQuery, meanEmbedding } from "./vector.js";
+import { cosineSimilarity, EMBEDDING_MODEL, embedQuery, meanEmbedding } from "./vector.js";
 export const DEFAULT_WEIGHTS = { bm25: 0.5, vector: 0.5 };
 const SNIPPET_RADIUS = 140;
 // Pulls a readable excerpt from a document body, centred on the earliest
@@ -67,7 +67,7 @@ function rankDocuments(db, queryTokens, queryEmbedding, opts) {
     const vectorRaw = new Map();
     let vectorUsed = false;
     if (queryEmbedding) {
-        for (const chunk of getAllChunks(db)) {
+        for (const chunk of getAllChunks(db, EMBEDDING_MODEL)) {
             if (!chunk.embedding)
                 continue;
             vectorUsed = true;
@@ -151,7 +151,7 @@ export function relatedSearch(db, path, options = {}) {
             error: new Error(`document not indexed: ${path} (try vault_reindex)`),
         };
     }
-    const chunkVectors = getChunksForPath(db, path)
+    const chunkVectors = getChunksForPath(db, path, EMBEDDING_MODEL)
         .map((c) => c.embedding)
         .filter((e) => e !== null);
     const queryEmbedding = meanEmbedding(chunkVectors);

package/dist/search/hybrid.js.map

@@ -1 +1 @@
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package/dist/search/index-state.d.ts

@@ -0,0 +1,17 @@
+export type IndexStatus = "ready" | "indexing" | "error";
+export interface IndexSnapshot {
+    status: IndexStatus;
+    done: number;
+    total: number;
+    error: string | null;
+    startedAt: string | null;
+    finishedAt: string | null;
+}
+export declare function getIndexStatus(): IndexSnapshot;
+export declare function markIndexing(): void;
+export declare function setIndexProgress(done: number, total: number): void;
+export declare function markIndexReady(): void;
+export declare function markIndexError(message: string): void;
+export declare function resetIndexState(): void;
+export declare function indexingBusyMessage(snapshot: IndexSnapshot): string;
+//# sourceMappingURL=index-state.d.ts.map

package/dist/search/index-state.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-state.d.ts","sourceRoot":"","sources":["../../src/search/index-state.ts"],"names":[],"mappings":"AASA,MAAM,MAAM,WAAW,GAAG,OAAO,GAAG,UAAU,GAAG,OAAO,CAAC;AAEzD,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,WAAW,CAAC;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;CAC3B;AAeD,wBAAgB,cAAc,IAAI,aAAa,CAE9C;AAED,wBAAgB,YAAY,IAAI,IAAI,CASnC;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,IAAI,CAGlE;AAED,wBAAgB,cAAc,IAAI,IAAI,CAOrC;AAED,wBAAgB,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAOpD;AAID,wBAAgB,eAAe,IAAI,IAAI,CAEtC;AAKD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,aAAa,GAAG,MAAM,CAKnE"}

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

@@ -1,10 +1,14 @@
 import { type Result } from "../frontmatter/types.js";
+export declare function isIndexFresh(vaultRoot: string): Promise<boolean>;
 export interface ReindexResult {
     documentCount: number;
     chunkCount: number;
     vectorEnabled: boolean;
     skipped: string[];
     indexedAt: string;
+    embeddedCount: number;
+    cacheHits: number;
+    orphansRemoved: number;
 }
 export interface ReindexOptions {
     onProgress?: (done: number, total: number) => void;

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

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