daftari 1.29.0 → 1.31.0

package/dist/storage/index-db.js

@@ -44,7 +44,13 @@ import { normalizeIsoDate } from "../utils/dates.js";
 // Bumped 4 → 5 to add FTS5 (`documents_fts`) and sqlite-vec (`embeddings_vec`)
 // virtual tables for SQL-native search. The index is a derived cache so the
 // bump triggers a clean rebuild (see openIndexDb); no in-place migration.
-const SCHEMA_VERSION = "7";
+// Bumped 7 → 8 to add the trail-extra columns (observations, contested_at,
+// contest_reason) to derives_from_edges, which became the authoritative edge
+// READ path (#236) and so must carry the full public edge shape.
+// Bumped 8 → 9 to add doc_links, the materialized inbound-link graph that
+// backs inline structural decay (#8) — orphan and deprecated-still-linked
+// answered with one indexed query at read/search time.
+const SCHEMA_VERSION = "9";
 // Meta key that records the dim at which `embeddings_vec` was created. Used
 // on every open to decide whether to rebuild the virtual table (provider
 // switch). The durable `embeddings` cache is per-(model, dim) so it survives
@@ -96,6 +102,12 @@ CREATE TABLE IF NOT EXISTS meta (
   key   TEXT PRIMARY KEY,
   value TEXT NOT NULL
 );
+CREATE TABLE IF NOT EXISTS doc_links (
+  source_path TEXT NOT NULL,
+  target_path TEXT NOT NULL,
+  PRIMARY KEY (source_path, target_path)
+);
+CREATE INDEX IF NOT EXISTS idx_doc_links_target ON doc_links(target_path);
 CREATE TABLE IF NOT EXISTS staged_actions (
   id                  TEXT PRIMARY KEY,
   action_type         TEXT NOT NULL,
@@ -123,6 +135,9 @@ CREATE TABLE IF NOT EXISTS derives_from_edges (
   last_age_decay TEXT NOT NULL,
   status         TEXT NOT NULL,
   direction_verdict TEXT NOT NULL DEFAULT 'directed',
+  observations   INTEGER NOT NULL DEFAULT 0,
+  contested_at   TEXT,
+  contest_reason TEXT,
   PRIMARY KEY (from_path, to_path)
 );
 CREATE INDEX IF NOT EXISTS idx_edges_from ON derives_from_edges(from_path);
@@ -290,12 +305,6 @@ export function clearEmbeddingsVec(db) {
 export function insertEmbeddingVec(db, contentHash, model, embedding) {
     db.prepare("INSERT INTO embeddings_vec(content_hash, model, embedding) VALUES (?, ?, ?)").run(contentHash, model, embeddingToBlob(embedding));
 }
-// Deletes the vec-mirror rows for a single content_hash. Used by the
-// orphan gc pass so the vec index never carries vectors whose chunks are
-// gone.
-function deleteEmbeddingsVecForHash(db, contentHash) {
-    db.prepare("DELETE FROM embeddings_vec WHERE content_hash = ?").run(contentHash);
-}
 // `expectedVecDim` is the active embedding provider's dim. If the persisted
 // `embeddings_vec` was created at a different dim (or doesn't exist yet),
 // it is dropped and recreated at the expected dim — the durable `embeddings`
@@ -377,7 +386,7 @@ export function openIndexDb(vaultRoot, expectedVecDim) {
 // cleared here — they are content-addressed and a subsequent gc pass deletes
 // only the orphaned ones, preserving the cache across reindexes.
 export function clearIndex(db) {
-    db.exec("DELETE FROM documents; DELETE FROM chunks;");
+    db.exec("DELETE FROM documents; DELETE FROM chunks; DELETE FROM doc_links;");
 }
 // Drops one document and all its chunks. Used by the write path to evict a
 // document's stale rows before re-inserting it: a plain INSERT OR REPLACE on
@@ -385,6 +394,45 @@ export function clearIndex(db) {
 export function deleteDocument(db, path) {
     db.prepare("DELETE FROM documents WHERE path = ?").run(path);
     db.prepare("DELETE FROM chunks WHERE path = ?").run(path);
+    // Outgoing links die with the doc. Inbound rows pointing AT it may remain
+    // (their sources still link here on disk); inboundLinkers joins documents
+    // on source_path, so a deleted source can never surface as a linker.
+    db.prepare("DELETE FROM doc_links WHERE source_path = ?").run(path);
+}
+// --- inbound-link graph (#8) ------------------------------------------------
+//
+// doc_links materializes the body-link graph at (re)index time so the read
+// and search paths can answer "who links here?" with one indexed query
+// instead of loading the whole vault (the exact cost #8 designs out). Rows
+// are derived and rebuildable — same ephemerality contract as everything
+// else in this file.
+// Replaces the outgoing link rows for one source document.
+export function replaceDocLinks(db, sourcePath, targets) {
+    db.prepare("DELETE FROM doc_links WHERE source_path = ?").run(sourcePath);
+    const insert = db.prepare("INSERT OR IGNORE INTO doc_links (source_path, target_path) VALUES (?, ?)");
+    for (const t of targets) {
+        if (t === sourcePath)
+            continue; // a self-link is not an inbound edge
+        insert.run(sourcePath, t);
+    }
+}
+// The documents whose bodies link to `targetPath`, with each linker's
+// lifecycle status (the deprecated-still-linked check needs it). Joined to
+// `documents` so a source deleted after its links were written can never
+// surface as a phantom linker.
+export function inboundLinkers(db, targetPath) {
+    return db
+        .prepare(`SELECT d.path AS path, d.status AS status
+         FROM doc_links AS l
+         JOIN documents AS d ON d.path = l.source_path
+        WHERE l.target_path = ?
+        ORDER BY d.path`)
+        .all(targetPath);
+}
+// Every indexed document path — the known-path universe outgoing-link
+// resolution runs against for a single-document incremental index.
+export function allDocumentPaths(db) {
+    return db.prepare("SELECT path FROM documents ORDER BY path").all().map((r) => r.path);
 }
 // --- Float32 <-> BLOB ------------------------------------------------------
 export function embeddingToBlob(vec) {
@@ -484,25 +532,38 @@ export function insertEmbedding(db, contentHash, model, embedding, createdAt, di
 // the vec-mirror counts piggy-back and are not reported separately.
 export function gcOrphanedEmbeddings(db) {
     // Collect the orphan hashes first so we can drop them from both stores in
-    // one pass. The `embeddings_vec` virtual table doesn't support correlated
-    // subqueries on its meta columns reliably, so we go through prepared
-    // deletes by hash.
+    // one transaction. `NOT EXISTS` with the `idx_chunks_content_hash` index lets
+    // sqlite short-circuit on the first matching chunk per hash, instead of
+    // materializing the full chunk-hash set the old uncorrelated `NOT IN
+    // (SELECT …)` built. `NOT IN` would also silently match nothing if any chunk
+    // hash were NULL; `NOT EXISTS` is null-safe.
     const orphans = db
-        .prepare(`SELECT content_hash
-         FROM embeddings
-        WHERE content_hash NOT IN (SELECT content_hash FROM chunks)`)
+        .prepare(`SELECT e.content_hash AS content_hash
+         FROM embeddings AS e
+        WHERE NOT EXISTS (
+                SELECT 1 FROM chunks AS c WHERE c.content_hash = e.content_hash
+              )`)
         .all();
     if (orphans.length === 0)
         return 0;
+    const hashes = orphans.map((o) => o.content_hash);
+    // Batch the deletes: one `DELETE … WHERE content_hash IN (?, ?, …)` per store
+    // per chunk of hashes, rather than a prepared statement fired once per orphan.
+    // Chunk under sqlite's bound-variable ceiling (SQLITE_MAX_VARIABLE_NUMBER,
+    // 999 on the builds better-sqlite3 ships). The `embeddings_vec` virtual table
+    // supports a plain IN-list on its `content_hash` meta column the same way the
+    // per-hash delete did.
+    const BATCH = 500;
     const drop = db.transaction(() => {
-        const dropEmb = db.prepare("DELETE FROM embeddings WHERE content_hash = ?");
-        for (const { content_hash } of orphans) {
-            dropEmb.run(content_hash);
-            deleteEmbeddingsVecForHash(db, content_hash);
+        for (let i = 0; i < hashes.length; i += BATCH) {
+            const batch = hashes.slice(i, i + BATCH);
+            const placeholders = batch.map(() => "?").join(", ");
+            db.prepare(`DELETE FROM embeddings WHERE content_hash IN (${placeholders})`).run(...batch);
+            db.prepare(`DELETE FROM embeddings_vec WHERE content_hash IN (${placeholders})`).run(...batch);
         }
     });
     drop();
-    return orphans.length;
+    return hashes.length;
 }
 export function setMeta(db, key, value) {
     db.prepare("INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)").run(key, value);
@@ -544,6 +605,47 @@ export function getDocument(db, path) {
     const row = db.prepare("SELECT * FROM documents WHERE path = ?").get(path);
     return row ? rowToDocument(row) : null;
 }
+// The collection that RBAC-gates access to `path`: the indexed row when
+// present; the path's first segment otherwise (the S1/#192 rule — key on
+// where the bytes live, never on a caller-declared string). `db` null means
+// the index is unavailable: gating degrades to the pure segment rule. That
+// fallback is only as fail-closed as the role config is sane — it does not
+// itself guard against blank or `..`-escaping paths; callers that need the
+// config-independent guard use tension-access's `sourceReadable`, which
+// canonicalizes and rejects such paths before resolving the collection.
+export function collectionForPath(db, path) {
+    if (db !== null) {
+        const doc = getDocument(db, path);
+        if (doc)
+            return doc.collection;
+    }
+    return path.split("/")[0] ?? "";
+}
+// Fetches the full document rows for a specific set of paths in one chunked
+// pass, instead of loading the whole `documents` table. The search hot path
+// uses this to scope the full-row read (content blob + JSON tag/token parse)
+// to the small candidate set the FTS/vector rankers already produced, rather
+// than paying O(vault) per query. The IN() list is chunked to stay under
+// SQLite's variable limit (default 999) — same pattern as
+// existingEmbeddingHashes. Order is unspecified (callers rank the result);
+// paths with no matching row are simply absent, and duplicate input paths
+// collapse to one row.
+export function getDocumentsByPaths(db, paths) {
+    if (paths.length === 0)
+        return [];
+    const out = [];
+    const BATCH = 500;
+    for (let start = 0; start < paths.length; start += BATCH) {
+        const slice = paths.slice(start, start + BATCH);
+        const placeholders = slice.map(() => "?").join(",");
+        const rows = db
+            .prepare(`SELECT * FROM documents WHERE path IN (${placeholders})`)
+            .all(...slice);
+        for (const r of rows)
+            out.push(rowToDocument(r));
+    }
+    return out;
+}
 // Converts a join row to the public chunk shape. The embedding is read iff
 // its stored dim matches the active provider's expected dim — a mismatch
 // would only happen if a row was written under different metadata than its
@@ -664,8 +766,9 @@ export function getStagedActionsByStatus(db, status) {
 export function upsertDerivesFromEdge(db, row) {
     db.prepare(`INSERT INTO derives_from_edges
        (from_path, to_path, strength, k_survived, first_observed, last_rederived,
-        last_age_decay, status, direction_verdict)
-     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+        last_age_decay, status, direction_verdict, observations, contested_at,
+        contest_reason)
+     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
      ON CONFLICT(from_path, to_path) DO UPDATE SET
        strength       = excluded.strength,
        k_survived     = excluded.k_survived,
@@ -673,7 +776,41 @@ export function upsertDerivesFromEdge(db, row) {
        last_rederived = excluded.last_rederived,
        last_age_decay = excluded.last_age_decay,
        status         = excluded.status,
-       direction_verdict = excluded.direction_verdict`).run(row.from_path, row.to_path, row.strength, row.k_survived, row.first_observed, row.last_rederived, row.last_age_decay, row.status, row.direction_verdict);
+       direction_verdict = excluded.direction_verdict,
+       observations   = excluded.observations,
+       contested_at   = excluded.contested_at,
+       contest_reason = excluded.contest_reason`).run(row.from_path, row.to_path, row.strength, row.k_survived, row.first_observed, row.last_rederived, row.last_age_decay, row.status, row.direction_verdict, row.observations, row.contested_at, row.contest_reason);
+}
+// One edge row matched in EITHER orientation: the stored (from_path, to_path)
+// is the derived OUTPUT orientation, which premise votes can flip, so a lookup
+// by pair must not assume the caller's order matches the stored order.
+export function getDerivesFromEdgePair(db, a, b) {
+    const row = db
+        .prepare(`SELECT * FROM derives_from_edges
+       WHERE (from_path = ? AND to_path = ?) OR (from_path = ? AND to_path = ?)`)
+        .get(a, b, b, a);
+    return row ?? null;
+}
+// Edge rows matching the given endpoint / status prefilters. `statusIn` is a
+// PREFILTER on the materialized status — the caller must recompute the live
+// aged status and re-filter; passing a conservative superset here is its job.
+export function listDerivesFromEdgeRows(db, filter = {}) {
+    const where = [];
+    const params = [];
+    if (filter.fromPath) {
+        where.push("from_path = ?");
+        params.push(filter.fromPath);
+    }
+    if (filter.toPath) {
+        where.push("to_path = ?");
+        params.push(filter.toPath);
+    }
+    if (filter.statusIn && filter.statusIn.length > 0) {
+        where.push(`status IN (${filter.statusIn.map(() => "?").join(", ")})`);
+        params.push(...filter.statusIn);
+    }
+    const sql = `SELECT * FROM derives_from_edges${where.length ? ` WHERE ${where.join(" AND ")}` : ""}`;
+    return db.prepare(sql).all(...params);
 }
 // Drops every edge row. Called at the start of a rebuild so a reindex never
 // leaves rows for edges the jsonl no longer reflects.

package/dist/storage/index-db.js.map

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package/dist/storage/local.d.ts

@@ -1,5 +1,11 @@
 import { type Result } from "../frontmatter/types.js";
-export declare function resolveVaultPath(vaultRoot: string, relativePath: string): Result<string, Error>;
+export declare function __clearRealRootCache(): void;
+export interface ResolvedVaultPath {
+    absPath: string;
+    relPath: string;
+}
+export declare function resolveVaultPath(vaultRoot: string, relativePath: string): Result<ResolvedVaultPath, Error>;
+export declare function canonicalVaultRelPath(vaultRoot: string, relativePath: string): Result<string, Error>;
 export declare function directoryExists(path: string): Promise<boolean>;
 export declare function readFile(absolutePath: string): Promise<Result<string, Error>>;
 export declare function listFiles(vaultRoot: string, pattern?: string): Promise<Result<string[], Error>>;

package/dist/storage/local.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"local.d.ts","sourceRoot":"","sources":["../../src/storage/local.ts"],"names":[],"mappings":"AAUA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AA+B/D,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAsB/F;AAED,wBAAsB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOpE;AAED,wBAAsB,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAQnF;AAID,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,OAAO,SAAY,GAClB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,KAAK,CAAC,CAAC,CAkBlC"}
+{"version":3,"file":"local.d.ts","sourceRoot":"","sources":["../../src/storage/local.ts"],"names":[],"mappings":"AAUA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAmD/D,wBAAgB,oBAAoB,IAAI,IAAI,CAE3C;AAaD,MAAM,WAAW,iBAAiB;IAChC,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;CACjB;AAKD,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,GACnB,MAAM,CAAC,iBAAiB,EAAE,KAAK,CAAC,CAsBlC;AAQD,wBAAgB,qBAAqB,CACnC,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,GACnB,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAIvB;AAED,wBAAsB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOpE;AAED,wBAAsB,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAQnF;AAID,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,OAAO,SAAY,GAClB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,KAAK,CAAC,CAAC,CAkBlC"}

package/dist/storage/local.js

@@ -37,8 +37,34 @@ function realpathConfined(p) {
         }
     }
 }
-// Resolves a vault-relative path to an absolute path, refusing anything that
-// escapes the vault root (path traversal) or resolves to the root itself.
+// Memoized real (symlink-resolved) vault roots, keyed by the lexically resolved
+// vaultRoot. The vault root does not change during a process, so realpath'ing it
+// once and reusing the result is safe — and it removes N redundant realpath
+// syscalls from the per-file loops in vaultIndex/vaultStatus (E4). ONLY the root
+// is cached; every untrusted caller-supplied TARGET is still fully realpath'd on
+// each call so the #142 symlink-escape protection is unchanged.
+const realRootCache = new Map();
+// Resolves and memoizes the real (symlink-resolved) vault root for a lexically
+// resolved root path. Returns null if the root cannot be resolved (same
+// fail-closed contract as realpathConfined).
+function resolveRealRoot(root) {
+    const cached = realRootCache.get(root);
+    if (cached !== undefined)
+        return cached;
+    const realRoot = realpathConfined(root);
+    if (realRoot === null)
+        return null;
+    realRootCache.set(root, realRoot);
+    return realRoot;
+}
+// Clears the memoized real-root cache. Exported for tests that create and tear
+// down temporary vault roots at the same absolute path within one process.
+export function __clearRealRootCache() {
+    realRootCache.clear();
+}
+// Resolves a vault-relative path, refusing anything that escapes the vault root
+// (path traversal) or resolves to the root itself. Returns both the absolute
+// target and the canonical vault-relative form (see ResolvedVaultPath).
 export function resolveVaultPath(vaultRoot, relativePath) {
     const root = resolve(vaultRoot);
     const target = resolve(root, relativePath);
@@ -51,7 +77,7 @@ export function resolveVaultPath(vaultRoot, relativePath) {
     // real paths for both the root and the target and re-check confinement. The
     // root is realpath'd too because the vault may itself sit under a symlinked
     // prefix (e.g. macOS /var → /private/var).
-    const realRoot = realpathConfined(root);
+    const realRoot = resolveRealRoot(root);
     const realTarget = realpathConfined(target);
     if (realRoot === null || realTarget === null) {
         return err(new Error(`path escapes vault root: ${relativePath}`));
@@ -60,7 +86,19 @@ export function resolveVaultPath(vaultRoot, relativePath) {
     if (realRel === "" || realRel.startsWith("..") || isAbsolute(realRel)) {
         return err(new Error(`path escapes vault root: ${relativePath}`));
     }
-    return ok(target);
+    return ok({ absPath: target, relPath: realRel });
+}
+// The realpath-canonical vault-relative form of a caller-supplied path
+// (trimmed), i.e. resolveVaultPath's relPath — the ONLY safe key for
+// looking up provenance, consumes, and read-log entries. Tools that anchor
+// a query on a caller string use this one helper; recomputing the relative
+// lexically diverges from the stored keys under a symlinked vault root
+// (#127/#128).
+export function canonicalVaultRelPath(vaultRoot, relativePath) {
+    const resolved = resolveVaultPath(vaultRoot, relativePath.trim());
+    if (!resolved.ok)
+        return resolved;
+    return ok(resolved.value.relPath);
 }
 export async function directoryExists(path) {
     try {

package/dist/storage/local.js.map

@@ -1 +1 @@
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package/dist/storage/sync.d.ts

@@ -0,0 +1,25 @@
+import { type Result } from "../frontmatter/types.js";
+import type { StorageBackend } from "./backend.js";
+export declare const MANIFEST_KEY = "meta/manifest.json";
+export interface SyncManifest {
+    version: 1;
+    files: Record<string, string>;
+}
+export interface SyncSummary {
+    uploaded: number;
+    deleted: number;
+    unchanged: number;
+    skippedSymlinks: number;
+    bytesUploaded: number;
+}
+export interface SyncOptions {
+    dryRun?: boolean;
+}
+export declare function syncVault(vaultRoot: string, backend: StorageBackend, options?: SyncOptions): Promise<Result<SyncSummary, Error>>;
+export interface RestoreSummary {
+    restored: number;
+    bytes: number;
+    skippedExcluded: number;
+}
+export declare function restoreVault(vaultRoot: string, backend: StorageBackend): Promise<Result<RestoreSummary, Error>>;
+//# sourceMappingURL=sync.d.ts.map

package/dist/storage/sync.d.ts.map

@@ -0,0 +1 @@
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