mcp-rag-memory 2.6.0 → 2.8.0

package/.env.example

@@ -20,6 +20,9 @@ RAG_MEMORY_HALF_LIFE_DAYS=14
 RAG_MAX_FILE_MB=10
 # RAG_ALLOWED_DIRS=C:\repo\a;C:\repo\b
 
+# Hybrid ranking: RRF constant for the default fusion (read at call time; default 60)
+# RAG_RRF_K=60
+
 # Session auto-sync / condensing (opencode plugin reads these from its own env)
 RAG_AUTOSYNC=1
 RAG_SESSION_CONDENSE=1

package/README.md

@@ -18,7 +18,7 @@ context **across sessions**.
 - **Context Management** — `remember` facts/decisions/preferences, `recall` them later (score-decayed by staleness), rate by importance, consolidate duplicates, filter by type/tag.
 - **Zero external APIs by default** — local hashing-embedder (1024-dim), built-in `node:sqlite`. Works fully offline. Optional `EMBEDDING_PROVIDER=transformers` for a higher-quality ONNX model.
 - **Safe ingestion** — content-hash deduplication, file size guard (`RAG_MAX_FILE_MB`) and an opt-in path allowlist (`RAG_ALLOWED_DIRS`).
-- **MCP server** — runs on stdio, 19 tools.
+- **MCP server** — runs on stdio, 21 tools.
 
 ## Quick start
 
@@ -27,7 +27,7 @@ Requires **Node.js ≥ 22.12** (for `node:sqlite` read-only handles and
 
 ```bash
 npm install
-npm test                 # 160 checks: unit + MCP round-trip via SDK client
+npm test                 # 238 checks: unit + MCP round-trip via SDK client
 npm run lint             # oxlint
 npm run typecheck        # src + scripts + .opencode/plugin
 npm run build            # compile to dist/
@@ -190,15 +190,17 @@ the global config to apply to every project.
 
 Restart opencode after any config change.
 
-## MCP tools (19)
+## MCP tools (21)
 
 | Group | Tool | Purpose |
 |-------|------|---------|
-| System | `system_stats` | DB dir, embedding backend, doc/memory counts |
+| System | `system_stats` | DB dir, embedding backend (incl. what the vector leg measures), store state, DB integrity, doc/memory counts |
+| Maintenance | `rag_reindex` | Re-embed every stored vector for the current model, migrating the store in place |
+| | `rag_backup` | Snapshot the store to a consistent SQLite file (VACUUM INTO — safe under WAL) and report its integrity; refuses to overwrite |
 | RAG ingest | `rag_ingest_text` | Store text as a knowledge document (dedup-aware) |
 | | `rag_ingest_file` | Store a file (`content_type` auto-detected) |
 | | `rag_ingest_dir` | Recursively ingest source files |
-| RAG query | `rag_search` | Hybrid (BM25 + vector) search, ranked chunks + scores |
+| RAG query | `rag_search` | Hybrid (BM25 + vector) search, ranked chunks + scores; `explain: true` adds per-leg scores, `alpha` tips the blend (0 = keyword-only, 1 = vector-only) |
 | | `rag_retrieve` | Ready-to-inject context block with token count |
 | RAG docs | `rag_list_documents`, `rag_document_stats` | Inventory (`rag_list_documents` is paginated: `limit` 1–1000, `offset`) |
 | | `rag_delete_document` | Remove a document + chunks + FTS rows |
@@ -269,9 +271,51 @@ first winning: the MCP client's `env` block → your shell environment → a
 `.env` and edit, or point at any file via `RAG_ENV_FILE`. The store defaults to
 `.rag-data/` in the working directory.
 
+## Changing the embedding model
+
+The store refuses to mix vector spaces: if `EMBEDDING_MODEL` changes, searching
+with new vectors against old ones would silently blend two spaces and return
+noise. `ensureDim` catches the mismatch and tells you to point `RAG_DB_DIR` at a
+fresh directory and re-ingest — correct, but for a memory store holding months of
+history that is a manual rebuild rather than a migration.
+
+`reindex` does the migration in place. It re-embeds every chunk and memory for the
+currently configured provider/model, then rewrites the store metadata.
+
+```bash
+# 1. install the optional provider
+npm i @huggingface/transformers
+
+# 2. migrate the existing store (documents' text is the source of truth)
+EMBEDDING_PROVIDER=transformers \
+EMBEDDING_MODEL=Xenova/all-MiniLM-L6-v2 \
+npm run cli -- reindex --batch 32
+
+# 3. bake the provider into .env so the server uses it from now on
+```
+
+Or over MCP: the `rag_reindex` tool takes the same `batch_size`.
+
+**How interruption behaves.** A half-migrated store mixes old and new vectors, so
+`reindex` marks the store `reindexing` for its whole duration and every search,
+recall and ingest refuses to run while that flag is set. This is deliberate: the
+failure mode of a partial migration is confident nonsense, and nothing about the
+results would reveal it. If the process dies mid-run, just run `reindex` again —
+the whole store is rewritten from text, so resuming is identical to starting over.
+`system_stats` reports `storeState` and the remediation if you hit this.
+
+Re-running is always safe: embedding is deterministic per model, so `reindex` is
+idempotent. On an empty store it is a no-op that just records the model.
+
+> **Upgrading the embedder version.** Bumping the bundled local embedder (e.g. the
+> 2.8 word-bi-gram `local-lexical-v2`) changes its model id, so an existing store is
+> treated as a different vector space and refuses to search until migrated. After
+> upgrading, run `npm run cli -- reindex` (or the `rag_reindex` tool) **once** — it
+> re-embeds in place. This is the same guard as changing `EMBEDDING_MODEL`, on purpose.
+
 ## Custom slash commands
 
-The 19 MCP tools are called by the AI automatically — but you can also
+The 21 MCP tools are called by the AI automatically — but you can also
 trigger them directly with custom commands. Sources (same name, project
 wins):
 
@@ -298,11 +342,16 @@ npm run cli -- recall "deployment schedule"
 npm run cli -- ingest-dir ./src/rag
 npm run cli -- search "vector similarity"
 npm run cli -- search "auth bug" --source opencode-db   # filter by source or doc-id
+npm run cli -- search "auth bug" --explain              # per-leg vector/keyword/RRF scores
+npm run cli -- search "client" --alpha 0               # keyword-only blend (0 = keyword, 1 = vector, default = RRF)
 npm run cli -- docs --limit 20 --offset 20            # paginated inventory
 npm run cli -- mem-context "database"
 npm run cli -- sessions              # list recent opencode sessions
 npm run cli -- sync-session ses_123  # ingest one session's inputs
 npm run cli -- sync-latest           # ingest the most recent session
+npm run cli -- reindex --batch 32    # re-embed all vectors for the current model
+npm run cli -- backup backups/v1.sqlite   # consistent snapshot (VACUUM INTO)
+npm run cli -- restore backups/v1.sqlite  # replace the store from a backup (stop the server first)
 npm run clean-db -- --force          # wipe ALL documents + memories (destructive)
 ```
 
@@ -359,30 +408,106 @@ The plugin needs an opencode restart to take effect.
 ## Performance & limits
 
 - **Search is brute-force cosine / FTS5 over every chunk**: `O(N)` per query
-  (exact, deterministic — good for a personal store of thousands of chunks).
-  ANN / HNSW indexing is planned scope (v3) for 100k+ chunks.
+    (exact, deterministic — good for a personal store of thousands of chunks).
+    ANN / HNSW indexing is planned scope (v3) for 100k+ chunks.
+- **The vector cache holds every vector in RAM**, uncapped and complete. Truncating
+    it would silently change which documents are findable, so the cache stays whole
+    and the server warns instead: 8 KB per row at the default 1024 dims, so 100k
+    chunks is roughly 800 MB. Tune the warning threshold with
+    `RAG_VECTOR_CACHE_WARN_MB` (default 256). Beyond a few hundred thousand chunks,
+    expect to prune rather than scale.
 - Keyword leg uses the FTS5 **trigram** tokenizer, so CJK text and
   Indonesian-style substring/inflection matching work without extra config.
   Consequence: keyword terms of **≤ 2 characters are skipped** (trigram needs
   3); the vector leg still covers them.
 - Vector embeddings are local hash-based (no external APIs, ~0 cost, offline).
-  They are tuned for short-phrase similarity, not full-document semantics.
+    They are tuned for short-phrase similarity, not full-document semantics.
+
+### What the vector leg actually measures
+
+This matters more than it sounds, so the server states it explicitly in
+`system_stats` (`embedding.vectorLeg`) rather than calling everything "semantic".
+
+| Provider | `vectorLeg` | Meaning |
+|---|---|---|
+| `local` (default) | `lexical` | Hashes character 1/2/3-grams **plus word bi-grams** into 1024 buckets. Scores **lexical and sub-word overlap** (word order now matters a little), not meaning. |
+| `transformers` | `semantic` | Real sentence embeddings from `EMBEDDING_MODEL`. Captures meaning. |
+
+Consequence for the default: `"cara fix login"` and `"masalah autentikasi"`
+share almost no n-grams, so the **vector** leg scores near zero even though they
+mean the same thing. Retrieval still works because the **FTS5 trigram** leg
+carries the query, and because the local embedder does respond to shared substrings
+and character shapes. What you should not expect from the default is
+paraphrase-level recall — restating a concept with different vocabulary is the
+known blind spot.
+
+To get true semantic recall, install the optional dependency and migrate in place:
+
+```bash
+npm i @huggingface/transformers
+EMBEDDING_PROVIDER=transformers EMBEDDING_MODEL=Xenova/all-MiniLM-L6-v2 npm run cli -- reindex
+```
+
+`reindex` rewrites every stored vector for the new model. See
+[Changing the embedding model](#changing-the-embedding-model).
+
+### Scoring & `min_score` calibration
+
+Two ordering modes, and `min_score` means something different in each:
+
+| Mode | How hits are ordered | What `score` / `min_score` is |
+|---|---|---|
+| **Default (RRF)** | Reciprocal-rank fusion over the vector and keyword rankings | The fused RRF contribution (`rrfScore`), a small number — top hits are typically `0.03`–`0.08`, so the practical floor is ~`0.01`–`0.03`. |
+| **`alpha` blend** | `score = alpha·vectorScore + (1−alpha)·keywordScore` | A real 0..1 relevance value — `alpha = 0` is keyword-only, `1` is vector-only, in between is a weighted average. `0.1`–`0.3` is a sensible default threshold. |
+
+- The RRF constant is `RAG_RRF_K` (default `60`); it is read **at call time**, so
+  raise it to widen the rank spread (harder to distinguish hits) or lower it to
+  sharpen it. With `alpha`, `min_score` runs against the blended value instead.
+- The keyword leg always reports a 0..1 normalised BM25 (`keywordScore`); the
+  vector leg reports cosine in `-1..1` (`vectorScore`). `explain` shows exactly
+  what fed the final number — see the table below.
+
+### Debugging a bad search
+
+`rag_search` accepts `explain: true` (CLI: `--explain`), which attaches the
+per-leg diagnostics to every hit:
+
+```jsonc
+{
+  "score": 0.71,          // final relevance, 0..1 — what min_score filters on
+  "legs": ["vector", "keyword"],
+  "explain": {
+    "vectorScore": 0.63,  // cosine similarity, -1..1
+    "keywordScore": 1.0,  // BM25 normalised against the best hit, 0..1
+    "rrfScore": 0.0246,   // fused contribution that decided the order
+    "vectorRank": 0,
+    "keywordRank": 2
+  }
+}
+```
+
+| Symptom | Likely cause |
+|---|---|
+| `legs: ["keyword"]`, no `vectorScore` | Only the trigram leg matched. Expected for paraphrase queries under the `local` provider. |
+| `legs: ["vector"]` with a low `vectorScore` | Lexical overlap only. Rephrase, or switch provider. |
+| `keywordScore` near 0 for every hit | The query terms are absent from the corpus, or under 3 characters. |
+| No hits at all | Lower `min_score`, or set `SEARCH_MODE=keyword` to isolate which leg is failing. |
 
 ## Architecture
 
 ```
 src/
-├── db/database.ts          node:sqlite (documents, chunks, memories, chunks_fts, meta)
+├── db/database.ts          node:sqlite (documents, chunks, memories, chunks_fts, meta) + integrity/backup/restore
 ├── rag/
-│   ├── embedder.ts         local hashing embedder (1024-d, FNV-1a, n-grams)
+│   ├── embedder.ts         local hashing embedder (1024-d, FNV-1a, word + char n-grams)
 │   ├── embeddings.ts       provider layer: local | transformers (optional dep)
 │   ├── chunker.ts          paragraph/code-aware chunking with overlap
-│   ├── vector-search.ts    vector cache + FTS5 BM25 + RRF hybrid scoring
+│   ├── vector-search.ts    vector cache + FTS5 BM25 + RRF hybrid scoring (alpha blend, RAG_RRF_K)
 │   └── pipeline.ts         async ingest/search/retrieve, dedup, guards, doc mgmt
 ├── session/transcript.ts   read opencode sessions (global+local DB), ingest inputs
-├── memory/memory.ts        remember / recall / consolidate + decay + prune
-├── mcp/rag-server.ts       MCP server (19 tools, stdio, npm bin)
-├── cli.ts                  CLI playground (incl. sync-session / sync-latest / sync-logs)
+├── memory/memory.ts        remember / recall / consolidate + decay + prune (last-activity anchored)
+├── mcp/rag-server.ts       MCP server (21 tools, stdio, npm bin)
+├── cli.ts                  CLI playground (incl. sync-session / sync-latest / backup / restore)
 └── test/test-all.ts        full test suite (unit + MCP round-trip)
 ```
 
@@ -398,7 +523,10 @@ Data lives in `.rag-data/rag.sqlite` (git-ignored).
 | `EMBEDDING_MODEL` | `Xenova/all-MiniLM-L6-v2` | Transformers model name |
 | `RAG_MAX_FILE_MB` | `10` | Reject files larger than this |
 | `RAG_ALLOWED_DIRS` | *(unset = anywhere)* | Semicolon/pipe/comma-separated allowed ingest roots |
+| `RAG_RRF_K` | `60` | RRF constant for default hybrid ranking (read at call time) |
 | `RAG_MEMORY_HALF_LIFE_DAYS` | `14` | Recall score decay half-life |
+| `RAG_DEDUP_MAX_VECTORS` | `500` | Above this many memories `consolidate` skips near-duplicate detection and reports `skippedDedup`. Raise it on a dedicated server (the pass is O(n²)) |
+| `RAG_VECTOR_CACHE_WARN_MB` | `256` | Warn when the in-memory vector cache exceeds this size |
 | `RAG_PRUNE` | `0` | Set `1` to allow `consolidate` to delete non-essential memories |
 | `RAG_PRUNE_IMPORTANCE` | `0.2` | Delete memories below this importance |
 | `RAG_PRUNE_AGE_DAYS` | `90` | ...and older than this (never-recalled only) |
@@ -523,7 +651,7 @@ can slow down the TUI. This repo ships exactly one plugin
 `npx … sync-latest` per 60s, spawned detached with `stdio: "ignore"` and
 `shell: false`. If it still costs too much, set `RAG_AUTOSYNC=0` (keeps the
 plugin, disables the auto-sync) or drop the `plugin` entry from
-`opencode.json` — the MCP server and its 19 tools keep working, you just have
+`opencode.json` — the MCP server and its 21 tools keep working, you just have
 to call `rag_sync_session` yourself.
 
 ---

package/dist/cli.js

@@ -9,7 +9,7 @@
  *   ingest-text  <title> <file|->              Ingest text (from file or stdin)
  *   ingest-file  <path>                        Ingest a single file
  *   ingest-dir   <dir>                         Ingest a directory
- *   search       <query>                       Semantic search over documents
+ *   search       <query> [--top-k N] [--min-score S] [--explain] [--alpha A] [--doc-id ID] [--source S]
  *   retrieve     <query>                       Retrieve context block
  *   docs                                      List documents
  *   doc-stats                                 Document stats
@@ -24,6 +24,9 @@
  *   memory-stats
  *   mem-context  <topic>
  *   stats                                       Everything
+ *   reindex    [--batch N]                      Re-embed all vectors for the current model
+ *   backup     [path]                          Snapshot the store to a consistent SQLite file
+ *   restore    <path>                          Replace the store from a backup (offline — stop the server first)
  *   sessions                                    List opencode sessions (recent first)
  *   sync-session <sessionId> [--limit N]        Ingest a session's user inputs to RAG
  *   sync-latest   [--limit N] [--dir PATH]      Ingest the most recent session (workspace-aware)
@@ -34,8 +37,10 @@ import "./env.js";
 import { ingestText, ingestFile, ingestDirectory, searchDocs, retrieve, listDocuments, deleteDocument, documentStats } from "./rag/pipeline.js";
 import { remember, recall, listMemories, getMemory, updateMemory, forget, consolidate, memoryStats, contextPrompt, MEMORY_TYPES } from "./memory/memory.js";
 import { ingestSession, ingestJsonlFile, ingestLogDir, ingestLatest, listOpenCodeSessions } from "./session/transcript.js";
-import { closeDB, STORAGE_DIR } from "./db/database.js";
+import { reindex } from "./rag/reindex.js";
+import { closeDB, STORAGE_DIR, backupStore, restoreStore } from "./db/database.js";
 import * as fs from "fs";
+import * as path from "path";
 async function main() {
     const [, , cmd, ...rest] = process.argv;
     if (!cmd) {
@@ -47,7 +52,7 @@ async function main() {
     closeDB();
 }
 function helpText() {
-    return `Commands: ingest-text|ingest-file|ingest-dir|search|retrieve|docs|doc-stats|rm-doc|remember|recall|memory-list|memory-get|memory-update|forget|consolidate|memory-stats|mem-context|stats|sessions|sync-session|sync-latest|sync-logs|ingest-jsonl`;
+    return `Commands: ingest-text|ingest-file|ingest-dir|search|retrieve|docs|doc-stats|rm-doc|remember|recall|memory-list|memory-get|memory-update|forget|consolidate|memory-stats|mem-context|stats|reindex|backup|restore|sessions|sync-session|sync-latest|sync-logs|ingest-jsonl`;
 }
 function assertMemoryType(type) {
     if (!MEMORY_TYPES.includes(type)) {
@@ -80,10 +85,14 @@ async function run(cmd, args) {
                 break;
             case "search": {
                 const parsed = parseOpts(args);
+                const alpha = toNum(parsed.opts.alpha, undefined);
+                if (alpha !== undefined && (alpha < 0 || alpha > 1)) {
+                    throw new Error("--alpha must be between 0 and 1");
+                }
                 out = await searchDocs(queryArg(parsed.positional), toNum(parsed.opts["top-k"], 10), toNum(parsed.opts["min-score"], 0.08), {
                     docId: parsed.opts["doc-id"],
                     source: parsed.opts.source,
-                });
+                }, parsed.opts.explain !== undefined, alpha);
                 break;
             }
             case "retrieve": {
@@ -181,6 +190,27 @@ async function run(cmd, args) {
             case "stats":
                 out = { documents: documentStats(), memories: memoryStats(), dbDir: STORAGE_DIR };
                 break;
+            case "reindex": {
+                const parsed = parseOpts(args);
+                out = await reindex({
+                    batchSize: toNum(parsed.opts.batch, undefined),
+                    onProgress: (p) => {
+                        if (p.total > 0) {
+                            process.stderr.write(`reindex ${p.phase}: ${p.done}/${p.total}\r`);
+                        }
+                    },
+                });
+                process.stderr.write("\n");
+                break;
+            }
+            case "backup": {
+                const target = args[0] ?? path.join(STORAGE_DIR, "backups", `rag-backup-${Date.now()}.sqlite`);
+                out = backupStore(target);
+                break;
+            }
+            case "restore":
+                out = restoreStore(requireArg(args[0], "restore <backup-file>"));
+                break;
             case "sessions": {
                 const parsed = parseOpts(args);
                 out = listOpenCodeSessions(toNum(parsed.opts.limit, 15) ?? 15, { directory: parsed.opts.dir });

package/dist/db/database.d.ts

@@ -11,6 +11,56 @@ export declare function packVector(v: Float64Array): Uint8Array;
 export declare function unpackVector(blob: Uint8Array | null): Float64Array | null;
 export declare function nowMs(): number;
 export declare function closeDB(): void;
+export interface IntegrityReport {
+    ok: boolean;
+    errorCount: number;
+    firstError?: string;
+}
+/**
+ * Surface-level check for one page of corruption (the default pass) on either
+ * the live store or a standalone file. Reading the store while another process
+ * writes is safe here: integrity_check takes its own snapshot.
+ */
+export declare function integrityCheck(targetPath?: string): IntegrityReport;
+export interface StoreCounts {
+    documents: number;
+    chunks: number;
+    memories: number;
+}
+export declare function storeCounts(db?: DatabaseSync): StoreCounts;
+export interface BackupReport extends StoreCounts {
+    path: string;
+    bytes: number;
+    integrity: IntegrityReport;
+}
+/**
+ * Consistent snapshot of the live store via `VACUUM INTO`. Unlike a raw file
+ * copy this works regardless of WAL state and never writes into the live DB.
+ * SQLite refuses to overwrite an existing target, which doubles as a built-in
+ * no-clobber guard for the tool surface.
+ */
+export declare function backupStore(target: string): BackupReport;
+export interface RestoreReport extends StoreCounts {
+    path: string;
+    restoredFrom: string;
+    integrity: IntegrityReport;
+}
+/**
+ * Replace the live store with a backup file, offline (run while no server is
+ * using the store). The current WAL journal is checkpointed and then discarded
+ * together with -shm before the copy, so a stale WAL belonging to the replaced
+ * database can never bleed into the restored one. The store is reopened and
+ * re-verified before returning; on failure it is left closed so a subsequent
+ * command surfaces the problem instead of running against a half state.
+ */
+export declare function restoreStore(source: string): RestoreReport;
+/** Health lamp for system_stats: runs integrity_check only on stores small enough that it cannot stall the server. */
+export declare function storeHealthSummary(): {
+    status: "ok" | "corrupt" | "deferred";
+    errorCount?: number;
+    firstError?: string;
+    reason?: string;
+};
 export declare function getEmbedDim(): number;
 export declare function setEmbedMeta(dim: number, model: string): void;
 /**
@@ -19,4 +69,12 @@ export declare function setEmbedMeta(dim: number, model: string): void;
  */
 export declare function ensureDim(vec: Float64Array, model: string): void;
 export declare function getEmbedModel(): string;
+/**
+ * `embed_state` is '' (or 'ready') for a coherent store and 'reindexing' while a
+ * vector-space migration is in flight.
+ */
+export declare function getEmbedState(): string;
+export declare function setEmbedState(state: string): void;
+/** Throws when the store is mid-reindex. Called from ensureDim, the shared gate. */
+export declare function assertEmbedStateReady(): void;
 //# sourceMappingURL=database.d.ts.map

package/dist/db/database.d.ts.map

@@ -1 +1 @@
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package/dist/db/database.js

@@ -173,6 +173,128 @@ export function closeDB() {
     _db = null;
     cachedDim = null;
 }
+/**
+ * Surface-level check for one page of corruption (the default pass) on either
+ * the live store or a standalone file. Reading the store while another process
+ * writes is safe here: integrity_check takes its own snapshot.
+ */
+export function integrityCheck(targetPath) {
+    // Opening a corrupt/foreign file can throw synchronously — that is exactly the
+    // case this helper exists to classify, so swallow it and report the failure.
+    let own;
+    try {
+        own = targetPath ? new DatabaseSync(path.resolve(targetPath), { readOnly: true }) : getDB();
+    }
+    catch (e) {
+        return { ok: false, errorCount: 1, firstError: String(e.message ?? e) };
+    }
+    let rows;
+    try {
+        rows = own.prepare("PRAGMA integrity_check").all();
+    }
+    catch (e) {
+        return { ok: false, errorCount: 1, firstError: String(e.message ?? e) };
+    }
+    finally {
+        if (targetPath)
+            own.close();
+    }
+    const errors = rows
+        .map((r) => String(r.integrity_check ?? Object.values(r)[0] ?? ""))
+        .filter((t) => t !== "ok");
+    if (errors.length === 0)
+        return { ok: true, errorCount: 0 };
+    return { ok: false, errorCount: errors.length, firstError: errors[0] };
+}
+export function storeCounts(db = getDB()) {
+    const one = (sql) => Number(db.prepare(sql).get().c);
+    return {
+        documents: one("SELECT COUNT(*) AS c FROM documents"),
+        chunks: one("SELECT COUNT(*) AS c FROM chunks"),
+        memories: one("SELECT COUNT(*) AS c FROM memories"),
+    };
+}
+/** Quote a path as a SQLite string literal (VACUUM INTO takes a literal, not a bound param). */
+function sqliteLiteral(value) {
+    return "'" + value.replace(/'/g, "''") + "'";
+}
+/**
+ * Consistent snapshot of the live store via `VACUUM INTO`. Unlike a raw file
+ * copy this works regardless of WAL state and never writes into the live DB.
+ * SQLite refuses to overwrite an existing target, which doubles as a built-in
+ * no-clobber guard for the tool surface.
+ */
+export function backupStore(target) {
+    const abs = path.resolve(target);
+    if (abs.toLowerCase() === DB_PATH.toLowerCase()) {
+        throw new Error("Backup target must not be the live store file");
+    }
+    fs.mkdirSync(path.dirname(abs), { recursive: true });
+    getDB().exec(`VACUUM INTO ${sqliteLiteral(abs)}`);
+    const counts = storeCounts();
+    return {
+        path: abs,
+        bytes: fs.statSync(abs).size,
+        documents: counts.documents,
+        chunks: counts.chunks,
+        memories: counts.memories,
+        integrity: integrityCheck(abs),
+    };
+}
+/**
+ * Replace the live store with a backup file, offline (run while no server is
+ * using the store). The current WAL journal is checkpointed and then discarded
+ * together with -shm before the copy, so a stale WAL belonging to the replaced
+ * database can never bleed into the restored one. The store is reopened and
+ * re-verified before returning; on failure it is left closed so a subsequent
+ * command surfaces the problem instead of running against a half state.
+ */
+export function restoreStore(source) {
+    const src = path.resolve(source);
+    if (!fs.existsSync(src) || !fs.statSync(src).isFile()) {
+        throw new Error(`Backup file not found: ${src}`);
+    }
+    if (src.toLowerCase() === DB_PATH.toLowerCase()) {
+        throw new Error("Source is the live store file itself; pick a backup copy");
+    }
+    try {
+        getDB().exec("PRAGMA wal_checkpoint(TRUNCATE);");
+    }
+    catch {
+        /* a closed or locked store has nothing to checkpoint */
+    }
+    closeDB();
+    try {
+        // -wal/-shm belong to the database being replaced; leaving them around lets
+        // SQLite replay a journal that has nothing to do with the restored file.
+        fs.rmSync(`${DB_PATH}-wal`, { force: true });
+        fs.rmSync(`${DB_PATH}-shm`, { force: true });
+        fs.copyFileSync(src, DB_PATH);
+        const db = getDB();
+        const integrity = integrityCheck();
+        const counts = storeCounts(db);
+        return { path: DB_PATH, restoredFrom: src, ...counts, integrity };
+    }
+    catch (e) {
+        throw new Error(`Restore failed (the store is closed; run any command to reopen it): ${e instanceof Error ? e.message : String(e)}`);
+    }
+}
+/** Health lamp for system_stats: runs integrity_check only on stores small enough that it cannot stall the server. */
+export function storeHealthSummary() {
+    const counts = storeCounts();
+    const rows = counts.documents + counts.chunks + counts.memories;
+    const max = 100_000;
+    if (rows > max) {
+        return {
+            status: "deferred",
+            reason: `store has ${rows} rows; run 'rag_backup' or 'cli backup' to verify integrity`,
+        };
+    }
+    const rep = integrityCheck();
+    if (rep.ok)
+        return { status: "ok", errorCount: 0 };
+    return { status: "corrupt", errorCount: rep.errorCount, firstError: rep.firstError };
+}
 /* ------------------------------------------------------------------ */
 /* Embedding dimension metadata                                        */
 /* ------------------------------------------------------------------ */
@@ -193,12 +315,19 @@ export function setEmbedMeta(dim, model) {
     db.prepare("INSERT INTO meta(key, value) VALUES ('embed_dim', ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value").run(String(dim));
     db.prepare("INSERT INTO meta(key, value) VALUES ('embed_model', ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value").run(model);
     cachedDim = dim;
+    // A completed migration restores the store to a coherent state.
+    setEmbedState("ready");
 }
 /**
  * Lock the store to one embedding dimension. Call after producing a vector.
  * Prevents silently mixing vectors of different models/providers.
  */
 export function ensureDim(vec, model) {
+    // A half-migrated store mixes old and new vectors: cosine across two spaces
+    // is meaningless and every search silently returns noise. Blocking here stops
+    // it at the one chokepoint every search and ingest already passes through,
+    // rather than letting a partial reindex look like a working store.
+    assertEmbedStateReady();
     const current = getEmbedDim();
     if (current === 0) {
         setEmbedMeta(vec.length, model);
@@ -223,4 +352,26 @@ export function getEmbedModel() {
     const r = getDB().prepare("SELECT value FROM meta WHERE key = 'embed_model'").get();
     return r ? r.value : "";
 }
+/**
+ * `embed_state` is '' (or 'ready') for a coherent store and 'reindexing' while a
+ * vector-space migration is in flight.
+ */
+export function getEmbedState() {
+    const r = getDB().prepare("SELECT value FROM meta WHERE key = 'embed_state'").get();
+    return r ? r.value : "";
+}
+export function setEmbedState(state) {
+    getDB()
+        .prepare("INSERT INTO meta(key, value) VALUES('embed_state', ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value")
+        .run(state);
+}
+/** Throws when the store is mid-reindex. Called from ensureDim, the shared gate. */
+export function assertEmbedStateReady() {
+    const state = getEmbedState();
+    if (state !== "" && state !== "ready") {
+        throw new Error(`Store is mid-reindex (embed_state=${state}): vectors from two embedding models are ` +
+            `mixed and search results would be meaningless. Run 'reindex' again to finish the ` +
+            `migration. Current store: ${STORAGE_DIR}.`);
+    }
+}
 //# sourceMappingURL=database.js.map

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