@andre.li/memoark 0.3.1

package/dist/sync/obsidian.js

@@ -0,0 +1,539 @@
+/**
+ * Obsidian vault bidirectional sync.
+ *
+ * Implements `memoark export --vault <path>` and `memoark import --vault <path>`.
+ * See spec: docs/specs/memoark-2026-06-04-obsidian-sync.md (v7).
+ */
+import { createHash } from "node:crypto";
+import { access, lstat, mkdir, open, readdir, readFile, rename, unlink, writeFile, } from "node:fs/promises";
+import { dirname, join, relative, resolve, sep } from "node:path";
+import { parse as yamlParse, stringify as yamlStringify } from "yaml";
+// ============================================================================
+// Constants
+// ============================================================================
+const RELATED_MARKER = "<!-- memoark:related -->";
+const TIMELINE_MARKER = "<!-- memoark:timeline -->";
+/** Unicode-safe slug regex (H3). */
+const SLUG_REGEX = /^[\p{L}\p{N}_-]+(\/[\p{L}\p{N}_-]+)*$/u;
+/** Windows reserved names (L6) — rejected on all platforms for portability. */
+const WINDOWS_RESERVED = new Set([
+    "con",
+    "prn",
+    "aux",
+    "nul",
+    "com1",
+    "com2",
+    "com3",
+    "com4",
+    "com5",
+    "com6",
+    "com7",
+    "com8",
+    "com9",
+    "lpt1",
+    "lpt2",
+    "lpt3",
+    "lpt4",
+    "lpt5",
+    "lpt6",
+    "lpt7",
+    "lpt8",
+    "lpt9",
+]);
+const MAX_SLUG_LENGTH = 200;
+/** Wikilink pattern: matches [[slug]] or [[slug|display]] with Unicode support. */
+const WIKILINK_REGEX = /\[\[([^\]|]+?)(?:\|[^\]]+?)?\]\]/gu;
+// ============================================================================
+// Section 1: serializePage (Spec §4.4)
+// ============================================================================
+/**
+ * Serialize a Page into Obsidian-compatible markdown.
+ *
+ * Fixes applied:
+ *   H1: explicit fields written AFTER `...page.frontmatter` so they cannot be
+ *       clobbered by user-supplied frontmatter that happens to share a key.
+ *   M1: `updated_at` is NOT written to frontmatter — it would change every export
+ *       even when content is identical, defeating incremental sync.
+ *   N3: rebuild `## Aliases` body section from `frontmatter.aliases` each time
+ *       (frontmatter is the single source of truth; the body section is derived).
+ */
+export function serializePage(page, tags, links, timeline, userEdited) {
+    const fm = {
+        // 1. spread page.frontmatter FIRST (low precedence — H1)
+        ...page.frontmatter,
+        // 2. explicit fields LAST (high precedence — H1)
+        title: page.title,
+        type: page.type,
+        slug: page.slug,
+        tags,
+        links: links.map((l) => ({ target: l.to_slug, type: l.link_type })),
+        content_hash: page.content_hash,
+        user_edited: userEdited,
+        // NOTE: updated_at intentionally omitted (M1)
+    };
+    // N3: rebuild Aliases section from frontmatter, not from body
+    const aliases = page.frontmatter.aliases ?? [];
+    const compiledWithoutAliases = stripAliasesSection(page.compiled_truth);
+    const bodyParts = [];
+    if (aliases.length > 0) {
+        bodyParts.push("## Aliases", "");
+        for (const alias of aliases) {
+            bodyParts.push(`- ${alias}`);
+        }
+        bodyParts.push("");
+    }
+    bodyParts.push(compiledWithoutAliases.trim());
+    if (links.length > 0) {
+        bodyParts.push("", "<!-- memoark:related -->", "");
+        for (const link of links) {
+            bodyParts.push(`- [[${link.to_slug}]]`);
+        }
+    }
+    if (timeline.length > 0) {
+        bodyParts.push("", "<!-- memoark:timeline -->", "");
+        bodyParts.push("> ⚠️ Timeline 为只读派生数据，编辑此处不会同步回 DB", "");
+        for (const entry of timeline) {
+            bodyParts.push(`- **${entry.date}**: ${entry.summary}`);
+        }
+    }
+    const body = bodyParts.join("\n");
+    const fmYaml = yamlStringify(fm).trimEnd();
+    return `---\n${fmYaml}\n---\n\n${body}\n`;
+}
+/**
+ * Strip `## Aliases\n\n- ...` section if it appears at the start of body.
+ *
+ * Only matches at body start so that mid-body Aliases-like headings stay intact.
+ */
+export function stripAliasesSection(body) {
+    const pattern = /^##\s+Aliases\s*\n+(?:- .+\n?)+\n*/;
+    return body.replace(pattern, "").trimStart();
+}
+/**
+ * Split body into three sections by HTML comment markers.
+ *
+ * Fixes:
+ *   M3: detect marker order reversal (timeline before related) and signal error.
+ */
+export function splitBody(body) {
+    const rIdx = body.indexOf(RELATED_MARKER);
+    const tIdx = body.indexOf(TIMELINE_MARKER);
+    // M3: timeline marker must come after related marker if both exist
+    if (rIdx >= 0 && tIdx >= 0 && tIdx < rIdx) {
+        return { mainBody: "", related: "", timeline: "", orderError: true };
+    }
+    let main = body;
+    let related = "";
+    let timeline = "";
+    // Split timeline first (later marker), then related
+    if (tIdx >= 0) {
+        timeline = main.slice(tIdx + TIMELINE_MARKER.length).trim();
+        main = main.slice(0, tIdx);
+    }
+    if (rIdx >= 0) {
+        related = main.slice(rIdx + RELATED_MARKER.length).trim();
+        main = main.slice(0, rIdx);
+    }
+    return { mainBody: main.trim(), related, timeline, orderError: false };
+}
+/** Validate slug: Unicode-safe + Windows reserved + length (H3 + L6). */
+export function isValidSlug(slug) {
+    if (!slug || slug.length === 0)
+        return false;
+    if (slug.length > MAX_SLUG_LENGTH)
+        return false;
+    if (!SLUG_REGEX.test(slug))
+        return false;
+    for (const segment of slug.split("/")) {
+        if (WINDOWS_RESERVED.has(segment.toLowerCase()))
+            return false;
+    }
+    return true;
+}
+/** Convert a file path (relative to vault root) to slug. */
+export function slugifyPath(relativePath) {
+    return relativePath.replace(/^\.\//, "").replace(/^\//, "").replace(/\.md$/i, "");
+}
+/** Extract all wikilink targets from text, stripping display suffix. */
+export function extractWikilinks(text) {
+    const results = [];
+    const re = new RegExp(WIKILINK_REGEX.source, WIKILINK_REGEX.flags);
+    for (const match of text.matchAll(re)) {
+        results.push(match[1].trim());
+    }
+    return results;
+}
+function parseFrontmatterAndBody(content) {
+    const match = content.match(/^---\n([\s\S]*?)\n---\n?([\s\S]*)$/);
+    if (!match) {
+        return { fm: {}, body: content };
+    }
+    const fm = (yamlParse(match[1]) ?? {});
+    return { fm, body: match[2] };
+}
+/**
+ * Parse a vault markdown file into the pieces needed for putPage / addTag / addLink.
+ *
+ * Fixes:
+ *   H2-incomplete: filter links by type — only obsidian and bare strings are
+ *                  taken as user-editable; pipeline-managed types (works_on,
+ *                  collaborates, etc.) are ignored here so they cannot be
+ *                  duplicated as obsidian-type edges on round-trip.
+ *   H4: inject user_edited=true into cleanMarkdown so putPage persists the lock.
+ *   M3: throw if body marker order is reversed.
+ *   M7: timeline section is NOT parsed (export-only).
+ *   L4: body `## Aliases` section is not interpreted — only frontmatter is.
+ */
+export function parseVaultFile(content, relativePath) {
+    const { fm, body } = parseFrontmatterAndBody(content);
+    const slugRaw = fm.slug ?? slugifyPath(relativePath);
+    if (!isValidSlug(slugRaw)) {
+        throw new Error(`invalid slug: ${slugRaw}`);
+    }
+    const slug = slugRaw;
+    const split = splitBody(body);
+    if (split.orderError) {
+        throw new Error("marker order incorrect: timeline appears before related");
+    }
+    // H2-incomplete: filter frontmatter links to obsidian-type only
+    const rawFmLinks = Array.isArray(fm.links) ? fm.links : [];
+    const fmLinks = [];
+    for (const item of rawFmLinks) {
+        if (typeof item === "string") {
+            fmLinks.push(item);
+        }
+        else if (item && typeof item === "object") {
+            const obj = item;
+            if (typeof obj.target === "string") {
+                const type = obj.type;
+                if (type === undefined || type === null || type === "obsidian") {
+                    fmLinks.push(obj.target);
+                }
+            }
+        }
+    }
+    // Wikilinks from main body (always treated as obsidian)
+    const bodyLinks = extractWikilinks(split.mainBody);
+    const links = Array.from(new Set([...fmLinks, ...bodyLinks]));
+    const tags = Array.isArray(fm.tags) ? fm.tags : [];
+    // Build clean frontmatter for putPage (strip sync-layer metadata)
+    const cleanFm = { ...fm };
+    delete cleanFm.slug;
+    delete cleanFm.tags;
+    delete cleanFm.links;
+    delete cleanFm.content_hash;
+    delete cleanFm.user_edited;
+    // H4: stamp user_edited=true
+    cleanFm.user_edited = true;
+    const cleanFmYaml = yamlStringify(cleanFm).trimEnd();
+    // M7: drop timeline section from main body; keep mainBody only
+    const cleanMarkdown = `---\n${cleanFmYaml}\n---\n\n${split.mainBody}\n`;
+    return { slug, cleanMarkdown, tags, links };
+}
+// ============================================================================
+// Section 3: Manifest I/O (Spec §4.7 + §7.8)
+// ============================================================================
+const MANIFEST_FILENAME = ".memoark-sync.json";
+const MANIFEST_VERSION = 2;
+/** Load the sync manifest from a vault. Returns null if missing or invalid. */
+export async function loadManifest(vaultPath) {
+    const path = join(vaultPath, MANIFEST_FILENAME);
+    try {
+        const raw = await readFile(path, "utf-8");
+        const parsed = JSON.parse(raw);
+        if (parsed.version !== MANIFEST_VERSION)
+            return null;
+        if (!parsed.pages || typeof parsed.pages !== "object")
+            return null;
+        return parsed;
+    }
+    catch {
+        // Missing, unreadable, or malformed — treat as no manifest
+        return null;
+    }
+}
+/**
+ * Atomically write the sync manifest (M8 + N2).
+ *
+ * Procedure:
+ *   1. open(tmpPath, "w") → write JSON → handle.sync() → handle.close()
+ *   2. rename(tmpPath, targetPath) — POSIX atomic
+ *   3. On error: close handle if open, unlink tmp
+ *
+ * Note: Node `fs.fsync()` takes a file descriptor, not a path. We use
+ * `FileHandle.sync()` which is the FileHandle API's wrapper around fsync(fd).
+ */
+export async function saveManifest(vaultPath, manifest) {
+    const targetPath = join(vaultPath, MANIFEST_FILENAME);
+    const tmpPath = `${targetPath}.tmp`;
+    let handle = null;
+    try {
+        handle = await open(tmpPath, "w");
+        await handle.writeFile(JSON.stringify(manifest, null, 2), "utf-8");
+        await handle.sync();
+        await handle.close();
+        handle = null;
+        await rename(tmpPath, targetPath);
+    }
+    catch (e) {
+        if (handle)
+            await handle.close().catch(() => { });
+        await unlink(tmpPath).catch(() => { });
+        throw e;
+    }
+}
+function sha256(content) {
+    return createHash("sha256").update(content).digest("hex");
+}
+function nowIso() {
+    return new Date().toISOString();
+}
+// ============================================================================
+// Section 5: exportToVault (Spec §5)
+// ============================================================================
+export async function exportToVault(stores, vaultPath, opts = {}) {
+    const result = { written: 0, skipped: 0, errors: [] };
+    // 1. Ensure vault directory exists
+    await mkdir(vaultPath, { recursive: true });
+    // 2. Load old manifest
+    const oldManifest = await loadManifest(vaultPath);
+    // 3. List all pages
+    const pages = await stores.pages.listPages({ limit: 100000 });
+    // 4. M6: batch pre-query tags / links / timeline
+    const [tagsBySlug, linksBySlug, timelineBySlug] = await Promise.all([
+        stores.tags.getAllTagsGrouped(),
+        stores.graph.getAllLinksGrouped(),
+        stores.timeline.getAllTimelineGrouped(),
+    ]);
+    // 5. Build new manifest as we go
+    const newManifest = {
+        version: 2,
+        last_sync_at: nowIso(),
+        last_sync_op: "export",
+        pages: {},
+    };
+    // 6. Per-page serialization
+    for (const page of pages) {
+        try {
+            const tags = tagsBySlug.get(page.slug) ?? [];
+            const links = linksBySlug.get(page.slug) ?? [];
+            const timeline = timelineBySlug.get(page.slug) ?? [];
+            const userEdited = oldManifest?.pages[page.slug]?.user_edited ?? false;
+            const content = serializePage(page, tags, links, timeline, userEdited);
+            const fileHash = sha256(content);
+            const previousFileHash = oldManifest?.pages[page.slug]?.file_hash;
+            const unchanged = !opts.force && previousFileHash === fileHash;
+            if (!unchanged && !opts.dryRun) {
+                const filePath = join(vaultPath, `${page.slug}.md`);
+                await mkdir(dirname(filePath), { recursive: true });
+                await writeFile(filePath, content, "utf-8");
+            }
+            newManifest.pages[page.slug] = {
+                file_hash: fileHash,
+                db_content_hash_at_last_sync: page.content_hash,
+                last_synced_at: newManifest.last_sync_at,
+                last_synced_op: "export",
+                user_edited: userEdited,
+            };
+            if (unchanged) {
+                result.skipped += 1;
+            }
+            else {
+                result.written += 1;
+            }
+        }
+        catch (e) {
+            result.errors.push({
+                slug: page.slug,
+                reason: e instanceof Error ? e.message : String(e),
+            });
+        }
+    }
+    // 7. Persist manifest
+    if (!opts.dryRun) {
+        await saveManifest(vaultPath, newManifest);
+    }
+    return result;
+}
+// ============================================================================
+// Section 6: importFromVault (Spec §6)
+// ============================================================================
+/**
+ * Recursively scan markdown files in vault. Defensive against symlinks (L8).
+ */
+async function scanMarkdownFiles(dir, vaultRoot, results = []) {
+    const entries = await readdir(dir, { withFileTypes: true });
+    for (const entry of entries) {
+        const fullPath = join(dir, entry.name);
+        // L8: refuse to follow symlinks
+        const stat = await lstat(fullPath);
+        if (stat.isSymbolicLink())
+            continue;
+        // Defensive: stay within vault boundary
+        const resolved = resolve(fullPath);
+        if (!resolved.startsWith(resolve(vaultRoot) + sep) && resolved !== resolve(vaultRoot)) {
+            continue;
+        }
+        if (entry.isDirectory()) {
+            if (entry.name.startsWith("."))
+                continue;
+            if (entry.name === "node_modules")
+                continue;
+            await scanMarkdownFiles(fullPath, vaultRoot, results);
+        }
+        else if (entry.isFile()) {
+            if (!entry.name.endsWith(".md"))
+                continue;
+            results.push(fullPath);
+        }
+    }
+    return results;
+}
+/**
+ * Read vault file content, returning null when the file is an iCloud
+ * placeholder or empty (L7 + N1).
+ */
+async function readVaultFile(filePath) {
+    // L7: check for iCloud placeholder sibling .filename.icloud
+    const dir = dirname(filePath);
+    const base = filePath.slice(dir.length + 1);
+    const placeholderPath = join(dir, `.${base}.icloud`);
+    try {
+        await access(placeholderPath);
+        return null;
+    }
+    catch {
+        // No placeholder — proceed
+    }
+    const content = await readFile(filePath, "utf-8");
+    // N1: only flag genuinely empty content (the v4 regex /^[ -]+/ was nonsense)
+    if (content.length === 0 || content.trim().length === 0) {
+        return null;
+    }
+    return content;
+}
+export async function importFromVault(stores, vaultPath, opts = {}) {
+    const result = {
+        imported: 0,
+        skipped: 0,
+        errors: [],
+        warnings: [],
+    };
+    // 1. Verify vault exists
+    await access(vaultPath);
+    // 2. Load existing manifest (may be null on first import)
+    const manifest = (await loadManifest(vaultPath)) ??
+        {
+            version: 2,
+            last_sync_at: nowIso(),
+            last_sync_op: "import",
+            pages: {},
+        };
+    // 3. Scan vault for markdown files
+    const files = await scanMarkdownFiles(vaultPath, vaultPath);
+    for (const filePath of files) {
+        const relPath = relative(vaultPath, filePath);
+        try {
+            const content = await readVaultFile(filePath);
+            if (content === null) {
+                result.warnings.push({
+                    slug: relPath,
+                    reason: "iCloud placeholder or empty file — skipping",
+                });
+                result.skipped += 1;
+                continue;
+            }
+            const fileHash = sha256(content);
+            // 4. Parse to extract slug (needed for hash comparison)
+            const parsed = parseVaultFile(content, relPath);
+            const slug = parsed.slug;
+            const previousFileHash = manifest.pages[slug]?.file_hash;
+            if (!opts.force && previousFileHash === fileHash) {
+                result.skipped += 1;
+                continue;
+            }
+            // 5. H5: detect DB-side changes between syncs
+            const existingPage = await stores.pages.getPage(slug);
+            const recordedDbHash = manifest.pages[slug]?.db_content_hash_at_last_sync;
+            if (!opts.force &&
+                existingPage &&
+                recordedDbHash &&
+                existingPage.content_hash !== recordedDbHash) {
+                result.warnings.push({
+                    slug,
+                    reason: "DB content changed since last sync — your vault edits will overwrite DB changes",
+                });
+                if (opts.strictConflict) {
+                    result.skipped += 1;
+                    continue;
+                }
+            }
+            if (opts.dryRun) {
+                result.imported += 1;
+                continue;
+            }
+            // 6. Per-file write sequence (M2 deferred — see Spec §7.9 note)
+            //
+            // NOTE: We do NOT wrap in pg.transaction() — PGlite's transaction uses
+            // a mutex on the single connection, and store methods using `this.pg.query`
+            // (instead of tx.query) would deadlock waiting for the mutex to release.
+            // Refactoring all store methods to accept tx is out of scope.
+            //
+            // Atomicity guarantee: NONE. We rely on idempotent upserts:
+            //   - putPage: INSERT ... ON CONFLICT UPDATE (idempotent)
+            //   - addTag: INSERT ... ON CONFLICT DO NOTHING (idempotent)
+            //   - addLink: INSERT ... ON CONFLICT UPDATE (idempotent)
+            //   - rechunk: DELETE + INSERT (eventual consistency; retry-safe)
+            //
+            // If the process crashes mid-write, the next `memoark import` run will
+            // re-process the file (file_hash will still differ) and reach a
+            // consistent state. Worst case: chunks briefly out of date.
+            const newPage = await stores.pages.putPage(slug, parsed.cleanMarkdown);
+            for (const tag of parsed.tags) {
+                await stores.tags.addTag(slug, tag);
+            }
+            // H2-incomplete: only add obsidian-typed links; do not touch
+            // pipeline-typed links (works_on, collaborates, mentions, etc.)
+            const existingLinks = await stores.graph.getLinks(slug);
+            const existingObsidian = new Set(existingLinks.filter((l) => l.link_type === "obsidian").map((l) => l.to_slug));
+            for (const target of parsed.links) {
+                if (existingObsidian.has(target))
+                    continue;
+                try {
+                    await stores.graph.addLink(slug, target, "obsidian", "from obsidian vault");
+                }
+                catch (linkErr) {
+                    // Target may not exist — warn, do not fail
+                    result.warnings.push({
+                        slug,
+                        reason: `addLink ${slug} → ${target}: ${linkErr instanceof Error ? linkErr.message : String(linkErr)}`,
+                    });
+                }
+            }
+            // M7: NOT processing timeline (export-only)
+            await stores.chunks.rechunk(newPage.id, newPage.compiled_truth);
+            manifest.pages[slug] = {
+                file_hash: fileHash,
+                db_content_hash_at_last_sync: newPage.content_hash,
+                last_synced_at: nowIso(),
+                last_synced_op: "import",
+                user_edited: true,
+            };
+            result.imported += 1;
+        }
+        catch (e) {
+            result.errors.push({
+                file: relPath,
+                reason: e instanceof Error ? e.message : String(e),
+            });
+        }
+    }
+    // 7. Persist manifest
+    if (!opts.dryRun) {
+        manifest.last_sync_at = nowIso();
+        manifest.last_sync_op = "import";
+        await saveManifest(vaultPath, manifest);
+    }
+    return result;
+}
+//# sourceMappingURL=obsidian.js.map

package/dist/sync/obsidian.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,84 @@
+{
+  "name": "@andre.li/memoark",
+  "version": "0.3.1",
+  "description": "Local-first personal memory extraction and storage",
+  "type": "module",
+  "bin": {
+    "memoark": "./bin/memoark.mjs"
+  },
+  "main": "./dist/cli.js",
+  "exports": {
+    ".": "./dist/cli.js"
+  },
+  "files": [
+    "dist/",
+    "bin/",
+    "README.md",
+    "README.en.md",
+    "LICENSE"
+  ],
+  "homepage": "https://github.com/AndreLYL/memoark#readme",
+  "bugs": {
+    "url": "https://github.com/AndreLYL/memoark/issues"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "dev": "bun src/cli.ts",
+    "test": "vitest run",
+    "test:watch": "vitest --watch",
+    "gen:assets": "node scripts/gen-embedded-assets.mjs",
+    "build": "node scripts/gen-embedded-assets.mjs && tsc && node scripts/post-build.mjs",
+    "compile": "node scripts/gen-embedded-assets.mjs && bun build --compile src/cli.ts --outfile dist-bin/memoark",
+    "typecheck": "tsc --noEmit",
+    "prepublishOnly": "npm run build",
+    "lint": "biome check src/ tests/",
+    "lint:fix": "biome check --fix src/ tests/",
+    "format": "biome format --write src/ tests/",
+    "serve": "bun src/cli.ts serve",
+    "web:dev": "cd web && bun run dev",
+    "web:build": "cd web && bun run build",
+    "web:preview": "cd web && bun run preview"
+  },
+  "dependencies": {
+    "@electric-sql/pglite": "^0.4.6",
+    "@modelcontextprotocol/sdk": "^1.29.0",
+    "commander": "^11.1.0",
+    "hono": "^4.12.23",
+    "ink": "^7.0.5",
+    "openai": "^6.39.0",
+    "react": "^19.2.7",
+    "react-devtools-core": "^6.1.5",
+    "yaml": "^2.3.4",
+    "zod": "^3.22.4"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^2.4.15",
+    "@types/bun": "latest",
+    "@types/node": "^25.9.1",
+    "@types/react": "^19.2.16",
+    "fast-glob": "^3.3.3",
+    "typescript": "^6.0.3",
+    "vitest": "^1.0.4"
+  },
+  "keywords": [
+    "knowledge-graph",
+    "signal-extraction",
+    "claude-code",
+    "codex",
+    "ai-agent",
+    "conversation-mining",
+    "cli"
+  ],
+  "author": "AndreLYL",
+  "license": "Apache-2.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/AndreLYL/memoark.git"
+  },
+  "engines": {
+    "node": ">=18.0.0",
+    "bun": ">=1.0.0"
+  }
+}