@owrede/vault-memory 2.2.0 → 2.3.0

package/CHANGELOG.md

@@ -14,6 +14,46 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 _Nothing yet._
 
+## [2.3.0] — 2026-07-01
+
+### Added
+
+- **Datacore/Dataview rendered indexing — foundation** (ADR-033). Phase 1 strips
+  Datacore/Dataview query source from indexed text so raw query blocks no longer
+  pollute search (`src/reader/datacore.ts`). Phase 2 adds migration 016
+  (`notes.rendered_source_hash`) as the schema foundation for indexing rendered
+  content supplied by the Obsidian plugin. _Note: later phases of ADR-033 are not
+  yet complete; this release ships the foundation only._
+
+### Fixed
+
+- **Incremental full-vault indexer now re-indexes changed notes** (#14). `indexVault`
+  in `incremental` mode decided whether to re-index from chunk count alone, so a note
+  whose body changed but already had chunks kept stale chunks/embeddings/sections/edges
+  while its `hash`/`content` were updated in place. The reindex decision now mirrors the
+  single-note indexer's three-way logic (hash-unchanged / frontmatter-only / body-changed),
+  and a latent foreign-key ordering bug (sections must be deleted before chunks) is fixed.
+- **MCP server version is derived from `package.json`** (#14). `server.ts` hardcoded
+  `VERSION = "1.0.0"`, so the server advertised the wrong version and sink provisioning
+  stamped a stale sentinel. A new `src/version.ts` is the single source of truth.
+- **Frontmatter long-string serialization** (#14). Long string values are written
+  single-line instead of being folded into a `>-` YAML block scalar that Obsidian's
+  Properties editor mishandles.
+
+### Changed
+
+- **`engines.node` narrowed to `>=22 <26`** (#14). Node 26+ has no `better-sqlite3`
+  prebuild for the new ABI and building from source currently fails. README prerequisites
+  updated accordingly.
+- **Release versions reconciled to 2.3.0** across `package.json`, `plugin/package.json`,
+  `plugin/manifest.json`, and README (#14).
+
+## [2.2.1] — 2026-06-29
+
+### Fixed
+
+- **Section identity is now content + context, not content alone (ADR-032, migration 015).** Two byte-identical sibling sections in *different* contexts (e.g. `# Q1 > ## Risks "TBD"` and `# Q2 > ## Risks "TBD"`) previously collapsed into one row under `UNIQUE(note_id, anchor)` — silently dropping the second — because the content-hash anchor excludes the ancestor chain. Section identity is now `(note_id, heading_path, anchor)`, so differently-placed identical sections persist as distinct rows. `anchor` stays a pure content hash (ADR-003 H-7 and the D-05 `source_hashes` contract are unchanged); `search-sections` dedup widened to match. Migration 015 swaps the unique index; a verbatim block repeated under the *same* parent still collapses (one citation). Existing DBs reconcile on the next `index --full`.
+
 ## [2.2.0] — 2026-06-29
 
 ### Added

package/README.md

@@ -3,7 +3,7 @@
 **Local-first, source-agnostic-ready agentic knowledge layer over your Obsidian notes,
 exposed to any MCP-aware agent.**
 
-> See [CHANGELOG.md](./CHANGELOG.md) for release history. Latest: **v2.0.0** — additive
+> See [CHANGELOG.md](./CHANGELOG.md) for release history. Latest: **v2.3.0** — additive
 > over v1.x; the 23 v1 tool names + input schemas are preserved byte-identical.
 
 ## 30-second example
@@ -198,7 +198,9 @@ vault-memory supports two engines, selectable **per vault**:
 
 ### Prerequisites
 
-- **Node.js >= 22** — runtime for the MCP server (`brew install node@22`).
+- **Node.js 22–25** (`>=22 <26`) — runtime for the MCP server (`brew install node@22`).
+  Node 26+ is not yet supported: the native `better-sqlite3` dependency has no
+  prebuild for the new ABI and building from source currently fails.
 - One or more Obsidian vaults; an MCP-aware client.
 - **Ollama engine only:** [Ollama](https://ollama.com) on `localhost:11434`
   (`brew install ollama && brew services start ollama`) + the `bge-m3` model

package/dist/cli.js

@@ -1320,7 +1320,7 @@ function backfillSectionsFromChunks(db) {
        @parent_id, @ord, @chunk_id_first, @chunk_id_last, @created_at)
   `);
   const lookupExistingSection = db.prepare(
-    "SELECT id FROM sections WHERE note_id = ? AND anchor = ?"
+    "SELECT id FROM sections WHERE note_id = ? AND heading_path = ? AND anchor = ?"
   );
   let backfilled = 0;
   const now = Date.now();
@@ -1356,7 +1356,11 @@ function backfillSectionsFromChunks(db) {
       if (info.changes > 0) {
         insertedIds.push(Number(info.lastInsertRowid));
       } else {
-        const existing2 = lookupExistingSection.get(note.id, s.anchor);
+        const existing2 = lookupExistingSection.get(
+          note.id,
+          JSON.stringify(s.heading_path),
+          s.anchor
+        );
         insertedIds.push(existing2 ? Number(existing2.id) : null);
       }
     }
@@ -1688,6 +1692,17 @@ function runMigration014(db, _ctx) {
       ON contract_audit(verb);
   `);
 }
+function runMigration015(db, _ctx) {
+  db.exec(
+    "DROP INDEX IF EXISTS sections_note_anchor; CREATE UNIQUE INDEX IF NOT EXISTS sections_note_headingpath_anchor ON sections(note_id, heading_path, anchor);"
+  );
+}
+function runMigration016(db, _ctx) {
+  const cols = db.prepare("PRAGMA table_info(notes)").all();
+  if (!cols.some((c) => c.name === "rendered_source_hash")) {
+    db.exec("ALTER TABLE notes ADD COLUMN rendered_source_hash TEXT");
+  }
+}
 var INITIAL_SCHEMA, MIGRATION_002_ALIASES, MIGRATION_003_FIX_DELETE_FKS, MIGRATION_004_VARIABLE_DIMS, MIGRATION_006_BODY_HASH, MIGRATION_007_DOC_URI_ADD, MIGRATIONS;
 var init_schema = __esm({
   "src/db/schema.ts"() {
@@ -1963,6 +1978,16 @@ CREATE INDEX IF NOT EXISTS idx_notes_doc_uri ON notes(doc_uri);
         version: 14,
         description: "contract_audit table \u2014 Phase 6 / CON-* / Q-AUD",
         run: runMigration014
+      },
+      {
+        version: 15,
+        description: "section identity = (note_id, heading_path, anchor) \u2014 context-aware, no longer collapse byte-identical siblings in different contexts (ADR-032 revised)",
+        run: runMigration015
+      },
+      {
+        version: 16,
+        description: "notes.rendered_source_hash \u2014 overlay marker for plugin-rendered Datacore content (ADR-033)",
+        run: runMigration016
       }
     ];
   }
@@ -3067,6 +3092,9 @@ var init_sections = __esm({
         this._getByAnchor = db.prepare(
           "SELECT * FROM sections WHERE note_id = ? AND anchor = ?"
         );
+        this._getByIdentity = db.prepare(
+          "SELECT * FROM sections WHERE note_id = ? AND heading_path = ? AND anchor = ?"
+        );
         this._findContainingChunk = db.prepare(
           // `chunk_id` is monotonically increasing per note; chunk_id_first
           // and chunk_id_last carve disjoint ranges (or both NULL for a
@@ -3090,6 +3118,7 @@ var init_sections = __esm({
       _deleteByNote;
       _getByNote;
       _getByAnchor;
+      _getByIdentity;
       _findContainingChunk;
       _countByNote;
       /**
@@ -3122,14 +3151,15 @@ var init_sections = __esm({
         return ids;
       }
       /**
-       * Insert one section, collision-safe. Returns the id of the row that
-       * now owns (note_id, anchor): the freshly inserted row, or — when a
-       * same-anchor sibling already won the unique slot — that surviving
-       * row's id (so callers can resolve parent_id linkage). Mirrors the
-       * backfill behavior in src/sections/backfill.ts. The live indexer
-       * uses this instead of `insertMany` so duplicate-anchor sibling
-       * headings can't abort the whole index run
-       * (see ISSUE-indexer-duplicate-anchor.md).
+       * Insert one section, collision-safe. Returns the id of the row that now
+       * owns the identity (note_id, heading_path, anchor): the freshly inserted
+       * row, or — when a same-context byte-identical sibling already won the
+       * unique slot — that surviving row's id (so callers can resolve parent_id
+       * linkage). Per ADR-032 (revised), a collision now requires BOTH same anchor
+       * AND same heading_path, so differently-placed identical sections persist as
+       * distinct rows. Mirrors src/sections/backfill.ts. The live indexer uses
+       * this instead of `insertMany` so duplicate sibling headings can't abort the
+       * whole index run (see ISSUE-indexer-duplicate-anchor.md).
        */
       insertOneResolving(r) {
         const info = this._insert.run({
@@ -3145,7 +3175,7 @@ var init_sections = __esm({
           created_at: Date.now()
         });
         if (info.changes > 0) return Number(info.lastInsertRowid);
-        const existing = this._getByAnchor.get(r.note_id, r.anchor);
+        const existing = this._getByIdentity.get(r.note_id, r.heading_path, r.anchor);
         return existing ? Number(existing.id) : null;
       }
       deleteByNote(noteId) {
@@ -5873,6 +5903,73 @@ var init_wikilinks2 = __esm({
   }
 });
 
+// src/reader/datacore.ts
+function stripDynamicViewBlocks(body) {
+  if (!body.includes("```") && !body.includes("~~~")) {
+    return { content: body, replaced: 0 };
+  }
+  const lines = body.split("\n");
+  const out = [];
+  let replaced = 0;
+  let i = 0;
+  while (i < lines.length) {
+    const line = lines[i];
+    const open2 = FENCE_OPEN_RE.exec(line);
+    if (open2) {
+      const indent = open2[1] ?? "";
+      const marker = open2[2] ?? "";
+      const lang = (open2[3] ?? "").toLowerCase();
+      const markerChar = marker[0];
+      const isDynamic = DYNAMIC_VIEW_LANGS.has(lang);
+      let j = i + 1;
+      let closed = false;
+      while (j < lines.length) {
+        const close = FENCE_OPEN_RE.exec(lines[j]);
+        if (close && (close[2] ?? "")[0] === markerChar && (close[2] ?? "").length >= marker.length && (close[3] ?? "") === "") {
+          closed = true;
+          break;
+        }
+        j++;
+      }
+      if (isDynamic) {
+        out.push(`${indent}${DATACORE_PLACEHOLDER}`);
+        replaced++;
+        i = closed ? j + 1 : lines.length;
+      } else {
+        out.push(line);
+        if (closed) {
+          for (let k = i + 1; k <= j; k++) out.push(lines[k]);
+          i = j + 1;
+        } else {
+          for (let k = i + 1; k < lines.length; k++) out.push(lines[k]);
+          i = lines.length;
+        }
+      }
+    } else {
+      out.push(line);
+      i++;
+    }
+  }
+  if (replaced === 0) return { content: body, replaced: 0 };
+  return { content: out.join("\n"), replaced };
+}
+var DYNAMIC_VIEW_LANGS, DATACORE_PLACEHOLDER, FENCE_OPEN_RE;
+var init_datacore = __esm({
+  "src/reader/datacore.ts"() {
+    "use strict";
+    init_esm_shims();
+    DYNAMIC_VIEW_LANGS = /* @__PURE__ */ new Set([
+      "datacore",
+      "datacorejsx",
+      "datacorejs",
+      "dataview",
+      "dataviewjs"
+    ]);
+    DATACORE_PLACEHOLDER = "[Datacore view]";
+    FENCE_OPEN_RE = /^(\s*)(`{3,}|~{3,})\s*([A-Za-z0-9_-]*)\s*$/;
+  }
+});
+
 // src/adapters/source/obsidian-fs/hash.ts
 import { createHash as createHash3 } from "crypto";
 function sha256(input) {
@@ -5925,9 +6022,11 @@ async function parseNote(absolutePath, vaultRoot) {
   const wikilinks = frontmatterLinks.length === 0 ? bodyLinks : mergeFrontmatterIntoBody(bodyLinks, frontmatterLinks);
   const wordCount = countWords2(content);
   const relativePath = toPosix2(path3.relative(path3.resolve(vaultRoot), path3.resolve(absolutePath)));
+  const indexedContent = stripDynamicViewBlocks(content).content;
   return {
     relativePath,
     content,
+    indexedContent,
     frontmatter,
     title,
     hash,
@@ -5971,6 +6070,7 @@ var init_parser = __esm({
     "use strict";
     init_esm_shims();
     init_wikilinks2();
+    init_datacore();
     init_hash();
   }
 });
@@ -6814,6 +6914,9 @@ async function indexVault(vault, options) {
         log(`  skipped (parse error): ${rel} \u2014 ${msg}`);
         continue;
       }
+      const previous = vault.db.notes.getByPath(parsed.relativePath);
+      const hashUnchanged = previous != null && previous.hash === parsed.hash;
+      const bodyUnchanged = previous != null && previous.body_hash != null && previous.body_hash === parsed.bodyHash;
       const upsert = vault.db.notes.upsertByPath({
         path: parsed.relativePath,
         content: parsed.content,
@@ -6826,24 +6929,28 @@ async function indexVault(vault, options) {
       });
       vault.db.notes.setStatus(upsert.id, extractStatus(parsed.frontmatter));
       vault.db.aliases.setForNote(upsert.id, extractAliases(parsed.frontmatter));
-      const noteExisted = !upsert.isNew;
-      const existing = noteExisted ? vault.db.notes.getById(upsert.id) : null;
       const chunkCount = vault.db.chunks.getByNote(upsert.id).length;
-      const needsReindex = mode === "full" || upsert.isNew || chunkCount === 0;
+      const bodyChanged = !hashUnchanged && !bodyUnchanged;
+      const needsReindex = mode === "full" || upsert.isNew || chunkCount === 0 || bodyChanged;
+      const frontmatterOnly = !upsert.isNew && !needsReindex && !hashUnchanged;
       if (upsert.isNew) notesIndexed++;
-      else if (needsReindex) notesUpdated++;
+      else if (needsReindex || frontmatterOnly) notesUpdated++;
       if (needsReindex) {
         parsedNotes.push({ parsed, noteId: upsert.id, needsReindex: true });
+      } else if (frontmatterOnly) {
+        vault.db.wikilinks.deleteByNote(upsert.id);
+        vault.db.edges.deleteByNote(upsert.id);
+        insertWikilinks(vault, upsert.id, parsed.wikilinks, firstPassResolver);
+        writeAllEdges(vault, upsert.id, parsed, firstPassResolver);
       }
-      void existing;
     }
     log(`${parsedNotes.length} notes need (re-)indexing`);
     for (const { parsed, noteId } of parsedNotes) {
+      vault.db.sections.deleteByNote(noteId);
       vault.db.chunks.deleteByNote(noteId);
       vault.db.wikilinks.deleteByNote(noteId);
       vault.db.edges.deleteByNote(noteId);
-      vault.db.sections.deleteByNote(noteId);
-      const chunks = chunkNote(parsed.content);
+      const chunks = chunkNote(parsed.indexedContent);
       if (chunks.length === 0) {
         insertWikilinks(vault, noteId, parsed.wikilinks, firstPassResolver);
         writeAllEdges(vault, noteId, parsed, firstPassResolver);
@@ -6860,7 +6967,7 @@ async function indexVault(vault, options) {
       }));
       const chunkIds = vault.db.chunks.insertBatch(noteId, chunkInputs);
       try {
-        buildSectionsForNote(vault, noteId, parsed.content, chunkIds);
+        buildSectionsForNote(vault, noteId, parsed.indexedContent, chunkIds);
       } catch (err) {
         const message = err instanceof Error ? err.message : String(err);
         console.error(
@@ -7197,7 +7304,7 @@ async function indexNote(options) {
   vault.db.chunks.deleteByNote(upsert.id);
   vault.db.wikilinks.deleteByNote(upsert.id);
   vault.db.edges.deleteByNote(upsert.id);
-  const chunks = chunkNote(parsed.content);
+  const chunks = chunkNote(parsed.indexedContent);
   if (chunks.length === 0) {
     insertWikilinks2(vault, upsert.id, parsed.wikilinks);
     writeAllEdges2(vault, upsert.id, parsed);
@@ -7224,7 +7331,7 @@ async function indexNote(options) {
     }))
   );
   try {
-    buildSectionsForNote(vault, upsert.id, parsed.content, chunkIds);
+    buildSectionsForNote(vault, upsert.id, parsed.indexedContent, chunkIds);
   } catch (err) {
     const message = err instanceof Error ? err.message : String(err);
     process.stderr.write(
@@ -7829,7 +7936,8 @@ async function writeNote(input) {
       };
     }
   }
-  const fileText = frontmatter !== null && Object.keys(frontmatter).length > 0 ? matter2.stringify(content, frontmatter) : content;
+  const yamlDumpOptions = { lineWidth: -1 };
+  const fileText = frontmatter !== null && Object.keys(frontmatter).length > 0 ? matter2.stringify(content, frontmatter, yamlDumpOptions) : content;
   input.onBeforeFsWrite?.();
   await atomicWriteFile(absPath, fileText);
   const written = await readExistingFile(absPath);
@@ -10756,7 +10864,7 @@ async function searchSections(deps, args2) {
     const resolution = deps.sectionForHit(hit.vault, hit.notePath, hit.chunkIdx);
     if (!resolution) continue;
     if (resolution.headingPath.length === 0) continue;
-    const key = `${resolution.noteId}#${resolution.anchor}`;
+    const key = `${resolution.noteId}#${resolution.headingPath.join("\0")}#${resolution.anchor}`;
     const existing = sectionMap.get(key);
     if (!existing) {
       sectionMap.set(key, {
@@ -16119,6 +16227,92 @@ var init_contracts2 = __esm({
   }
 });
 
+// package.json
+var package_default;
+var init_package = __esm({
+  "package.json"() {
+    package_default = {
+      name: "@owrede/vault-memory",
+      version: "2.3.0",
+      description: "Local-first semantic memory MCP server for Obsidian vaults",
+      type: "module",
+      license: "MIT",
+      workspaces: [
+        "plugin"
+      ],
+      repository: {
+        type: "git",
+        url: "git+https://github.com/owrede/vault-memory.git"
+      },
+      bin: {
+        "vault-memory": "dist/cli.js"
+      },
+      files: [
+        "dist",
+        "README.md",
+        "LICENSE",
+        "CHANGELOG.md"
+      ],
+      engines: {
+        node: ">=22 <26"
+      },
+      scripts: {
+        build: "tsup",
+        dev: "tsx watch src/cli.ts",
+        start: "node dist/cli.js",
+        test: "vitest run",
+        "test:watch": "vitest",
+        lint: "tsc --noEmit",
+        "lint:adapters": "sh scripts/lint-adapters.sh",
+        "lint:check": 'sh scripts/check-fixture-privacy.sh && sh scripts/lint-no-telemetry.sh && sh scripts/lint-adapters.sh && tsc --noEmit && prettier --check "src/**/*.ts"',
+        format: 'prettier --write "src/**/*.ts"',
+        "eval:baseline": "vitest run evals/v1-baseline/baseline.test.ts",
+        "eval:snapshot": "node evals/v1-baseline/dump-tools.mjs > evals/v1-baseline/tools-list.snapshot.json && node evals/v1-baseline/dump-resources.mjs > evals/v1-baseline/resources-list.snapshot.json",
+        "eval:smoketest": "npm run build && node scripts/smoketest-non-claude.mjs",
+        release: "node scripts/release.mjs",
+        "sync-marketplace": "node scripts/sync-marketplace.mjs"
+      },
+      dependencies: {
+        "@huggingface/tokenizers": "^0.1.3",
+        "@modelcontextprotocol/sdk": "^1.29.0",
+        "better-sqlite3": "^11.7.0",
+        chokidar: "^4.0.1",
+        "cross-spawn": "^7.0.6",
+        graphology: "^0.26.0",
+        "graphology-communities-louvain": "^2.0.2",
+        "gray-matter": "^4.0.3",
+        "onnxruntime-node": "^1.26.0",
+        seedrandom: "^3.0.5",
+        "smol-toml": "^1.3.1",
+        "sqlite-vec": "^0.1.6",
+        yaml: "^2.9.0",
+        zod: "^4.4.3"
+      },
+      devDependencies: {
+        "@types/better-sqlite3": "^7.6.12",
+        "@types/node": "^22.10.0",
+        "@types/seedrandom": "^3.0.8",
+        prettier: "^3.4.0",
+        tsup: "^8.3.5",
+        tsx: "^4.19.2",
+        typescript: "^5.7.0",
+        vitest: "^2.1.8"
+      }
+    };
+  }
+});
+
+// src/version.ts
+var VERSION;
+var init_version = __esm({
+  "src/version.ts"() {
+    "use strict";
+    init_esm_shims();
+    init_package();
+    VERSION = package_default.version;
+  }
+});
+
 // src/server.ts
 var server_exports = {};
 __export(server_exports, {
@@ -17200,7 +17394,7 @@ async function serve(options = {}) {
 `);
   });
 }
-var VERSION, MEMORY_AUTO_DISCOVERY_FOLDER;
+var MEMORY_AUTO_DISCOVERY_FOLDER;
 var init_server = __esm({
   "src/server.ts"() {
     "use strict";
@@ -17239,7 +17433,7 @@ var init_server = __esm({
     init_brief2();
     init_assembly2();
     init_contracts2();
-    VERSION = "1.0.0";
+    init_version();
     MEMORY_AUTO_DISCOVERY_FOLDER = "_memory";
   }
 });