@monoes/monomindcli 2.14.0 → 2.15.0

package/dist/src/knowledge/document-pipeline.js

@@ -1,925 +1,30 @@
 /**
- * Document Pipeline — wires text extraction, chunking, embedding, and SQLite storage
- * into an end-to-end ingest/search/export pipeline for the Second Brain.
+ * Document Pipeline — the Second Brain's end-to-end ingest/search/export path,
+ * and the single import point for it.
+ *
+ * The implementation lives in focused modules; this file is the public surface
+ * every caller (CLI commands, MCP tools, the dashboard, the eval harness)
+ * imports from, so the map is here:
+ *
+ *  - `document-types.ts`    the shapes: IngestResult, KnowledgeExcerpt,
+ *                           DocumentMeta, ReconcileReport.
+ *  - `document-store.ts`    which store a scope writes to, and the lazy memory
+ *                           bridge that reaches it.
+ *  - `document-chunking.ts` text → heading-anchored, context-enriched chunks
+ *                           (and the spans that make one citable).
+ *  - `document-index.ts`    the append-only metadata log: versions,
+ *                           tombstones, lookups, superseded filtering,
+ *                           filesystem reconciliation.
+ *  - `document-ingest.ts`   file → extracted → chunked → stored → committed.
+ *  - `document-search.ts`   query → live chunks, decorated for citation.
+ *  - `okf-bundle.ts`        export to / import from a portable OKF bundle.
  *
  * @module v1/cli/knowledge/document-pipeline
  */
-import * as crypto from 'node:crypto';
-import * as fs from 'node:fs';
-import * as os from 'node:os';
-import * as path from 'node:path';
-import { DOC_EXTENSIONS, extractText } from '../capabilities/cap-documents.js';
-// Static import is safe and deliberate: memory-bridge imports only node builtins
-// at module scope (everything heavy is lazy), and the project-root rule must not
-// be duplicated — two copies of "which directory is this project" is exactly the
-// bug this default exists to fix.
-import { getProjectRoot } from '../memory/memory-bridge.js';
-const DEFAULT_CHUNK_SIZE = 3200;
-const DEFAULT_OVERLAP = 400;
-// Head-of-chunk cap for text served by searchKnowledge — chunks are
-// heading-anchored, so the head carries the most relevant content.
-const SEARCH_EXCERPT_TEXT_CAP = 800;
-// Inline fallback identical to @monoes/memory's knowledge/document-chunker.ts —
-// used only if the dynamic import below fails (package not installed/built).
-// Keep in sync if the shared chunker's boundary-snapping logic changes.
-const HEADING_LINE_RE = /^#{1,6} /;
-const FENCE_LINE_RE = /^\s{0,3}(`{3,}|~{3,})/;
-function fenceTogglesInline(text) {
-    const toggles = [];
-    let lineStart = 0;
-    while (lineStart <= text.length) {
-        const eol = text.indexOf('\n', lineStart);
-        const line = text.slice(lineStart, eol === -1 ? undefined : eol);
-        if (FENCE_LINE_RE.test(line))
-            toggles.push(lineStart);
-        if (eol === -1)
-            break;
-        lineStart = eol + 1;
-    }
-    return toggles;
-}
-function inFenceInline(toggles, pos) {
-    let lo = 0, hi = toggles.length;
-    while (lo < hi) {
-        const mid = (lo + hi) >> 1;
-        if (toggles[mid] <= pos)
-            lo = mid + 1;
-        else
-            hi = mid;
-    }
-    return (lo & 1) === 1;
-}
-function lastHeadingBefore(text, pos, toggles) {
-    let i = text.lastIndexOf('\n#', pos - 1);
-    while (i !== -1) {
-        const eol = text.indexOf('\n', i + 1);
-        const line = text.slice(i + 1, eol === -1 ? undefined : eol);
-        if (HEADING_LINE_RE.test(line) && !inFenceInline(toggles, i + 1))
-            return line.replace(/^#+ /, '').trim();
-        i = i > 0 ? text.lastIndexOf('\n#', i - 1) : -1; // fromIndex -1 clamps to 0 — would loop on a match at 0
-    }
-    const firstEol = text.indexOf('\n');
-    const firstLine = firstEol === -1 ? text : text.slice(0, firstEol);
-    return HEADING_LINE_RE.test(firstLine) &&
-        !inFenceInline(toggles, 0) &&
-        firstEol !== -1 &&
-        firstEol < pos
-        ? firstLine.replace(/^#+ /, '').trim()
-        : null;
-}
-function chunkDocumentInline(docId, text) {
-    if (text.includes('\r\n'))
-        text = text.replace(/\r\n/g, '\n');
-    if (text.length === 0)
-        return [];
-    const toggles = fenceTogglesInline(text);
-    const chunks = [];
-    let startChar = 0;
-    let chunkIndex = 0;
-    while (startChar < text.length) {
-        let endChar = Math.min(startChar + DEFAULT_CHUNK_SIZE, text.length);
-        let brokeAtHeading = false;
-        if (endChar < text.length) {
-            const windowStart = Math.max(startChar, endChar - Math.floor(DEFAULT_CHUNK_SIZE * 0.2));
-            const window = text.slice(windowStart, endChar);
-            let h = window.lastIndexOf('\n#');
-            while (h !== -1) {
-                const eol = window.indexOf('\n', h + 1);
-                const line = window.slice(h + 1, eol === -1 ? undefined : eol);
-                if (HEADING_LINE_RE.test(line) &&
-                    windowStart + h > startChar &&
-                    !inFenceInline(toggles, windowStart + h + 1))
-                    break;
-                h = h > 0 ? window.lastIndexOf('\n#', h - 1) : -1;
-            }
-            if (h !== -1 && windowStart + h > startChar) {
-                endChar = windowStart + h + 1;
-                brokeAtHeading = true;
-            }
-            else {
-                let lastParagraph = window.lastIndexOf('\n\n');
-                while (lastParagraph > 0 && inFenceInline(toggles, windowStart + lastParagraph + 1)) {
-                    lastParagraph = window.lastIndexOf('\n\n', lastParagraph - 1);
-                }
-                if (lastParagraph === 0 && inFenceInline(toggles, windowStart + 1))
-                    lastParagraph = -1;
-                if (lastParagraph !== -1)
-                    endChar = windowStart + lastParagraph + 2;
-            }
-        }
-        let chunkText = text.slice(startChar, endChar);
-        const heading = lastHeadingBefore(text, startChar + 1, toggles);
-        if (heading && !HEADING_LINE_RE.test(chunkText.trimStart()))
-            chunkText = `§ ${heading}\n${chunkText}`;
-        chunks.push({
-            chunkId: `${docId}:${chunkIndex}`,
-            docId,
-            text: chunkText,
-            startChar,
-            endChar,
-            chunkIndex,
-        });
-        chunkIndex++;
-        if (endChar >= text.length)
-            break;
-        startChar += brokeAtHeading
-            ? Math.max(1, endChar - startChar)
-            : Math.max(1, endChar - startChar - DEFAULT_OVERLAP);
-    }
-    return chunks;
-}
-async function chunkDocument(docId, text) {
-    try {
-        const mod = await import('@monoes/memory');
-        return mod.chunkDocument(docId, text, DEFAULT_CHUNK_SIZE, DEFAULT_OVERLAP);
-    }
-    catch {
-        return chunkDocumentInline(docId, text);
-    }
-}
-// ── Contextual chunk enrichment (item 6a) ─────────────────────────
-// Prepend a situating blurb per chunk before embedding: full heading
-// path + doc title + doc summary. No LLM, no network.
-//
-// The chunker's `§ heading` prefix (line 105) provides only the nearest
-// leaf heading. This replaces it with doc-level context so the embedding
-// model can distinguish "Memory Coordination" in a hooks doc from
-// "Memory Coordination" in a concepts doc.
-//
-// Applied at INGEST TIME (after chunking, before embedding), so:
-//  - Works identically regardless of which chunker ran (inline or @monoes/memory)
-//  - Works identically for both better-sqlite3 and sql.js (pure string ops)
-//  - Zero dependencies, zero network
-const SECTION_PREFIX_RE = /^§ [^\n]+\n/;
-/** Cap on the situating summary prepended to each chunk, ellipsis included. */
-const SUMMARY_MAX_CHARS = 120;
-function extractDocTitle(text, filePath) {
-    const eol = text.indexOf('\n');
-    const first = eol === -1 ? text : text.slice(0, eol);
-    return HEADING_LINE_RE.test(first)
-        ? first.replace(/^#+ /, '').trim()
-        : path.basename(filePath, path.extname(filePath)).replace(/[-_]/g, ' ');
-}
-function extractDocSummary(text) {
-    const lines = text.split('\n');
-    let inFence = false;
-    const parts = [];
-    for (const line of lines) {
-        if (FENCE_LINE_RE.test(line)) {
-            inFence = !inFence;
-            continue;
-        }
-        if (inFence)
-            continue;
-        if (HEADING_LINE_RE.test(line)) {
-            if (parts.length > 0)
-                break;
-            continue;
-        }
-        const t = line.trim();
-        if (!t || /^[|=-]/.test(t)) {
-            if (parts.length > 0)
-                break;
-            continue;
-        }
-        parts.push(t.startsWith('>') ? t.replace(/^>\s*/, '') : t);
-    }
-    const joined = parts.join(' ');
-    // Truncate with an ellipsis so a clipped summary is visibly clipped. The bare
-    // 150-char slice this replaces gave no signal that anything was cut, which
-    // read as a complete sentence to both a human and the embedding model.
-    return joined.length > SUMMARY_MAX_CHARS
-        ? `${joined.slice(0, SUMMARY_MAX_CHARS - 3).trimEnd()}...`
-        : joined;
-}
-function buildHeadingHierarchy(text, toggles) {
-    const out = [];
-    const eol0 = text.indexOf('\n');
-    const line0 = eol0 === -1 ? text : text.slice(0, eol0);
-    const firstLevel = line0.match(/^(#{1,6}) /)?.[1]?.length;
-    if (firstLevel !== undefined && !inFenceInline(toggles, 0)) {
-        out.push({
-            level: firstLevel,
-            text: line0.replace(/^#+ /, '').trim(),
-            offset: 0,
-        });
-    }
-    let i = text.indexOf('\n#', 0);
-    while (i !== -1) {
-        const ls = i + 1;
-        const e = text.indexOf('\n', ls);
-        const line = text.slice(ls, e === -1 ? undefined : e);
-        const level = line.match(/^(#{1,6}) /)?.[1]?.length;
-        if (level !== undefined && !inFenceInline(toggles, ls)) {
-            out.push({
-                level,
-                text: line.replace(/^#+ /, '').trim(),
-                offset: ls,
-            });
-        }
-        i = text.indexOf('\n#', ls);
-    }
-    return out;
-}
-function headingPathAt(hierarchy, pos) {
-    const stack = [];
-    for (const h of hierarchy) {
-        if (h.offset >= pos)
-            break;
-        while (stack.length > 0 && stack[stack.length - 1].level >= h.level)
-            stack.pop();
-        stack.push(h);
-    }
-    return stack.map((s) => s.text);
-}
-/**
- * Replace each chunk's `§ heading` prefix with a richer situating blurb:
- *   § <doc title> · <full heading path>
- *   <doc summary for non-first chunks>
- *
- * First chunks that start with their own heading are left untouched (the
- * heading IS the context). The summary line is omitted for the first
- * chunk since it is adjacent to the summary text anyway.
- */
-function enrichChunks(chunks, fullText, filePath) {
-    if (chunks.length === 0)
-        return chunks;
-    const toggles = fenceTogglesInline(fullText);
-    const hierarchy = buildHeadingHierarchy(fullText, toggles);
-    const title = extractDocTitle(fullText, filePath);
-    const summary = extractDocSummary(fullText);
-    return chunks.map((c) => {
-        let text = c.text;
-        // First chunk starting with its own heading — the heading IS the context
-        if (c.chunkIndex === 0 && HEADING_LINE_RE.test(text.trimStart()))
-            return c;
-        // Strip the old § leaf-heading prefix; we replace it with a richer one
-        text = text.replace(SECTION_PREFIX_RE, '');
-        const hpath = headingPathAt(hierarchy, c.startChar + 1);
-        const parts = [];
-        // Title + full heading path
-        if (hpath.length > 0 && hpath[0] !== title) {
-            parts.push(`§ ${title} · ${hpath.join(' > ')}`);
-        }
-        else if (hpath.length > 1) {
-            parts.push(`§ ${hpath.join(' > ')}`);
-        }
-        else {
-            parts.push(`§ ${title}`);
-        }
-        // Summary for non-first chunks — they are far from the doc intro
-        if (c.chunkIndex > 0 && summary) {
-            const snip = summary.length > 120 ? `${summary.slice(0, 117)}...` : summary;
-            parts.push(snip);
-        }
-        return { ...c, text: `${parts.join('\n')}\n${text}` };
-    });
-}
-// ── Constants ──────────────────────────────────────────────────────
-const KNOWLEDGE_NS_PREFIX = 'knowledge:';
-const METADATA_FILE = 'doc-metadata.jsonl';
-// Global brain constants — canonical definitions live in memory-bridge.ts
-// (GLOBAL_BRAIN / GLOBAL_BRAIN_DIR); duplicated here because the bridge is
-// imported lazily and these are needed synchronously.
-const GLOBAL_BRAIN_SENTINEL = '@global';
-const globalBrainRoot = () => process.env.MONOMIND_GLOBAL_BRAIN_DIR || path.join(os.homedir(), '.monomind', 'global-brain');
-/** scope 'global' routes to the personal cross-project store. */
-const isGlobalScope = (scope) => scope === 'global';
-const effectiveRoot = (scope, rootDir) => isGlobalScope(scope) ? globalBrainRoot() : rootDir;
-const storeDbPath = (scope) => isGlobalScope(scope) ? GLOBAL_BRAIN_SENTINEL : undefined;
-const IGNORE_DIRS = new Set([
-    'node_modules',
-    '.git',
-    'dist',
-    '.monomind',
-    '.claude',
-    '.next',
-    '__pycache__',
-    '.venv',
-    'vendor',
-]);
-const MAX_FILE_SIZE = 50 * 1024 * 1024; // 50MB
-// ── Helpers ────────────────────────────────────────────────────────
-function namespace(scope) {
-    return `${KNOWLEDGE_NS_PREFIX}${scope}`;
-}
-function contentHash(content) {
-    return crypto.createHash('sha256').update(content).digest('hex');
-}
-function metadataPath(rootDir) {
-    const dir = path.join(rootDir, '.monomind', 'knowledge');
-    fs.mkdirSync(dir, { recursive: true });
-    return path.join(dir, METADATA_FILE);
-}
-function readMetadata(rootDir) {
-    const file = metadataPath(rootDir);
-    if (!fs.existsSync(file))
-        return [];
-    // Last-wins per (filePath, scope): the file is append-only under concurrent
-    // ingests (session-start detached reindex + a manual `doc ingest` can
-    // overlap), so duplicates are expected and the newest record is truth.
-    // Corrupt lines (torn concurrent writes) are skipped, not fatal.
-    const latest = new Map();
-    for (const l of fs.readFileSync(file, 'utf-8').split('\n')) {
-        if (!l.trim())
-            continue;
-        try {
-            const m = JSON.parse(l);
-            latest.set(`${m.filePath} ${m.scope}`, m);
-        }
-        catch {
-            /* torn line */
-        }
-    }
-    // chunkCount -1 records are removal tombstones (see removeMetadataEntry)
-    const live = [...latest.values()].filter((m) => m.chunkCount >= 0);
-    // Occasional compaction: append-only + tombstones grow without bound; when
-    // the log gets big, rewrite it deduped (atomic rename — a concurrent append
-    // in the tiny window loses only its own record and self-heals on re-ingest).
-    try {
-        if (fs.statSync(file).size > 1024 * 1024) {
-            const tmp = `${file}.${process.pid}.compact`;
-            fs.writeFileSync(tmp, live.map((r) => JSON.stringify(r)).join('\n') + (live.length ? '\n' : ''), 'utf-8');
-            fs.renameSync(tmp, file);
-        }
-    }
-    catch {
-        /* compaction is best-effort */
-    }
-    return live;
-}
-function appendMetadata(rootDir, meta) {
-    fs.appendFileSync(metadataPath(rootDir), `${JSON.stringify(meta)}\n`, 'utf-8');
-}
-function removeMetadataEntry(rootDir, filePath, scope) {
-    const file = metadataPath(rootDir);
-    if (!fs.existsSync(file))
-        return;
-    // Tombstone by APPEND (chunkCount -1) instead of read-filter-rewrite — the
-    // rewrite raced concurrent appends and silently dropped them.
-    appendMetadata(rootDir, {
-        filePath,
-        scope,
-        contentHash: '',
-        chunkCount: -1,
-        indexedAt: new Date().toISOString(),
-        size: 0,
-    });
-}
-function toFileEntry(filePath) {
-    const stat = fs.statSync(filePath);
-    return {
-        path: filePath,
-        absolutePath: path.resolve(filePath),
-        extension: path.extname(filePath).toLowerCase(),
-        size: stat.size,
-        modified: stat.mtime,
-        created: stat.birthtime,
-    };
-}
-// ── Lazy bridge import ─────────────────────────────────────────────
-let _bridge;
-async function getBridge() {
-    if (_bridge === null)
-        return null;
-    if (_bridge)
-        return _bridge;
-    try {
-        _bridge = await import('../memory/memory-bridge.js');
-        return _bridge;
-    }
-    catch {
-        _bridge = null;
-        return null;
-    }
-}
-// ── Core Pipeline ──────────────────────────────────────────────────
-export async function ingestDocument(filePath, scope = 'shared', rootDir = getProjectRoot(), _metadataCache) {
-    const resolved = path.resolve(filePath);
-    const ext = path.extname(resolved).toLowerCase();
-    // AppleDouble resource forks (`._name.md`) are binary macOS sidecars, not
-    // documents. The directory walk has skipped dotfiles since 3e429194
-    // (2026-07-19), but that walk is only ONE of six callers that reach this
-    // function — the CLI `doc ingest`, the MCP `knowledge_ingest` tool, the
-    // dashboard's live fs.watch and its polling sweep, the eval harness, and
-    // `ingestDirectory` all land here, and four of them had no guard at all.
-    //
-    // Guarding at the boundary covers every caller at once, including callers
-    // added later. Guarding at each call site covers only the ones we thought to
-    // enumerate — which is how two `._` files reached the live index despite a
-    // working guard in the walk.
-    //
-    // Measured on this repo 2026-07-28: 96 `._` entries in the live index, 91 of
-    // them shadowing a real document of the same name and competing with it for
-    // top-k slots. That is a direct Recall@5/MRR@10 loss, not wasted storage.
-    if (isResourceFork(resolved)) {
-        return {
-            filePath: resolved,
-            chunksIndexed: 0,
-            scope,
-            skipped: true,
-            error: 'AppleDouble resource fork',
-        };
-    }
-    if (!DOC_EXTENSIONS.has(ext)) {
-        return {
-            filePath: resolved,
-            chunksIndexed: 0,
-            scope,
-            skipped: true,
-            error: `unsupported extension: ${ext}`,
-        };
-    }
-    if (!fs.existsSync(resolved)) {
-        return { filePath: resolved, chunksIndexed: 0, scope, skipped: true, error: 'file not found' };
-    }
-    const stat = fs.statSync(resolved);
-    if (stat.size > MAX_FILE_SIZE) {
-        return {
-            filePath: resolved,
-            chunksIndexed: 0,
-            scope,
-            skipped: true,
-            error: 'file too large (>50MB)',
-        };
-    }
-    rootDir = effectiveRoot(scope, rootDir);
-    const meta = _metadataCache ?? readMetadata(rootDir);
-    const existing = meta.find((m) => m.filePath === resolved && m.scope === scope);
-    let fullContent;
-    try {
-        const entry = toFileEntry(resolved);
-        fullContent = await extractText(entry);
-    }
-    catch (err) {
-        return { filePath: resolved, chunksIndexed: 0, scope, skipped: false, error: String(err) };
-    }
-    if (!fullContent || fullContent.trim().length === 0) {
-        return {
-            filePath: resolved,
-            chunksIndexed: 0,
-            scope,
-            skipped: true,
-            error: 'no text extracted',
-        };
-    }
-    const hash = contentHash(fullContent);
-    if (existing && existing.contentHash === hash) {
-        return { filePath: resolved, chunksIndexed: existing.chunkCount, scope, skipped: true };
-    }
-    // NOTE: the previous version's metadata record is deliberately NOT tombstoned
-    // here. `readMetadata` is last-wins per (filePath, scope), so appending the
-    // new record below already supersedes the old one — the tombstone was a no-op
-    // on the success path and destructive on the failure path: it retired a
-    // perfectly good previous index before knowing whether the replacement would
-    // land, so a failed re-ingest left the document with NO live version at all.
-    const docId = `${scope}:${resolved}`;
-    const rawChunks = await chunkDocument(docId, fullContent);
-    // monolean: [re-enabled] item 2 shipped 768d gte-modernbert-base — capacity handles enrichment
-    const chunks = enrichChunks(rawChunks, fullContent, resolved);
-    const bridge = await getBridge();
-    let indexed = 0;
-    for (const chunk of chunks) {
-        const key = `doc:${hash}:${chunk.chunkIndex}`;
-        if (bridge) {
-            try {
-                const storeResult = await bridge.bridgeStoreEntry({
-                    key,
-                    value: chunk.text,
-                    namespace: namespace(scope),
-                    generateEmbeddingFlag: true,
-                    tags: ['document', ext, `src:${resolved}`],
-                    upsert: true,
-                    dbPath: storeDbPath(scope),
-                });
-                if (storeResult?.success)
-                    indexed++;
-            }
-            catch (e) {
-                if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                    console.error(`[ingestDocument] failed to store chunk ${chunk.chunkIndex} of ${resolved}:`, e);
-            }
-        }
-    }
-    // Commit the document version ONLY when EVERY chunk stored. Recording the
-    // content hash after a partial store was the worse half of this bug: the
-    // hash check above then skipped the file on every future ingest, so the
-    // chunks that failed were never retried — a permanently, silently
-    // half-indexed document feeding knowledge retrieval with no signal at all.
-    // (Total failure was already handled; partial success was not.)
-    //
-    // Not committing is what makes a retry work: chunk keys are
-    // `doc:<contentHash>:<index>` and stores are upserts, so re-ingesting the
-    // same bytes rewrites the same keys and fills the gaps. Until it succeeds the
-    // partially-written chunks sit under a hash that is not live, and superseded
-    // filtering keeps them out of search (see `liveContentHashes`).
-    const complete = indexed === chunks.length;
-    if (complete) {
-        appendMetadata(rootDir, {
-            filePath: resolved,
-            contentHash: hash,
-            chunkCount: indexed,
-            indexedAt: new Date().toISOString(),
-            scope,
-            size: stat.size,
-        });
-    }
-    return {
-        filePath: resolved,
-        chunksIndexed: indexed,
-        scope,
-        skipped: false,
-        ...(complete
-            ? {}
-            : indexed > 0
-                ? {
-                    partial: true,
-                    error: `partial store: ${indexed}/${chunks.length} chunks — version not committed, re-ingest to repair`,
-                }
-                : {
-                    error: bridge
-                        ? 'all chunk stores failed'
-                        : 'memory bridge unavailable — nothing indexed',
-                }),
-    };
-}
-export async function ingestDirectory(dirPath, scope = 'shared', opts) {
-    const scanDir = path.resolve(dirPath);
-    const rootDir = path.resolve(opts?.rootDir ?? getProjectRoot());
-    const files = [];
-    function walk(dir, depth = 0) {
-        if (depth > 10)
-            return;
-        let entries;
-        try {
-            entries = fs.readdirSync(dir, { withFileTypes: true });
-        }
-        catch {
-            return;
-        }
-        for (const entry of entries) {
-            // Skip dotfiles/dot-dirs (incl. exFAT `._*` junk) — except `.monodesign`,
-            // whose critique snapshots are markdown worth surfacing in the Second Brain.
-            if (entry.name.startsWith('.') && entry.name !== '.monodesign')
-                continue;
-            const full = path.join(dir, entry.name);
-            if (entry.isDirectory()) {
-                if (!IGNORE_DIRS.has(entry.name))
-                    walk(full, depth + 1);
-            }
-            else if (entry.isFile()) {
-                const ext = path.extname(entry.name).toLowerCase();
-                if (DOC_EXTENSIONS.has(ext))
-                    files.push(full);
-            }
-        }
-    }
-    walk(scanDir);
-    const metadataCache = readMetadata(rootDir);
-    const result = {
-        filesProcessed: 0,
-        filesSkipped: 0,
-        totalChunks: 0,
-        errors: [],
-        results: [],
-    };
-    for (let i = 0; i < files.length; i++) {
-        opts?.onProgress?.(files[i], i, files.length);
-        const r = await ingestDocument(files[i], scope, rootDir, metadataCache);
-        result.results.push(r);
-        if (r.skipped) {
-            result.filesSkipped++;
-        }
-        else {
-            result.filesProcessed++;
-            result.totalChunks += r.chunksIndexed;
-        }
-        if (r.error && !r.skipped) {
-            result.errors.push(`${r.filePath}: ${r.error}`);
-        }
-    }
-    return result;
-}
-// ── Search ─────────────────────────────────────────────────────────
-/** Small additive boost so project knowledge wins ties against the global
- *  brain — local context is more likely to be what the user means. */
-const PROJECT_SCOPE_BOOST = 0.05;
-// ── Superseded-version filtering ───────────────────────────────────
-//
-// Chunk keys are `doc:<contentHash>:<chunkIndex>`. Re-ingesting a changed file
-// produces a NEW contentHash, so its chunks land under new keys — the previous
-// version's rows are never touched (`removeDocument` only tombstones metadata;
-// the bridge exposes no delete-by-prefix). The store therefore accumulates every
-// version a document has ever had, and all of them stay searchable.
-//
-// Measured on this repo's own store (2026-07-26): 9,067 `doc:`-keyed rows in
-// `knowledge:shared` spanning 798 distinct content hashes, of which only 139
-// are current — 8,542 rows (94.2%) are orphaned older versions.
-//
-// Nothing is deleted here. The current-hash set from doc-metadata.jsonl is used
-// to decide what search RETURNS; `includeSuperseded` puts the old versions back
-// (flagged `superseded: true`) for anyone who wants document history.
-/** Content hashes of the documents currently indexed under `rootDir`. */
-export function liveContentHashes(rootDir) {
-    const live = new Set();
-    for (const m of readMetadata(rootDir))
-        if (m.contentHash)
-            live.add(m.contentHash);
-    return live;
-}
-/** True when a metadata log exists under `rootDir`.
- *
- * An empty live-hash set has two very different causes: the log is missing (we
- * cannot judge what is current) or the log exists and every document has been
- * removed (nothing is current). Collapsing them made `doc remove` of the LAST
- * document a no-op — the tombstoned chunks came straight back in search.
- *
- * Reads the path directly instead of via `metadataPath`, which mkdir's. */
-export function hasKnowledgeMetadata(rootDir) {
-    return fs.existsSync(path.join(rootDir, '.monomind', 'knowledge', METADATA_FILE));
-}
-/**
- * True when `key` is a document chunk whose version is no longer current.
- * Non-`doc:` keys are never superseded. When no metadata is available nothing
- * is filtered, because "no metadata" must not read as "everything is stale".
- *
- * `metadataPresent` defaults to the old `live.size > 0` heuristic so existing
- * two-argument callers keep their exact behaviour; pass `hasKnowledgeMetadata`
- * to also filter correctly once the last document has been removed.
- */
-export function isSupersededKey(key, live, metadataPresent = live.size > 0) {
-    if (!key?.startsWith('doc:'))
-        return false;
-    if (!metadataPresent)
-        return false;
-    return !live.has(key.split(':')[1] ?? '');
-}
-/** How many rows to ask the backend for per requested result when superseded
- *  filtering is active — most rows in a long-lived store are old versions, so
- *  a 1:1 fetch would return an almost-empty page. */
-const SUPERSEDED_OVERFETCH = 20;
-const SUPERSEDED_OVERFETCH_CAP = 300;
-export function supersededOverfetchLimit(limit, live) {
-    if (live.size === 0)
-        return limit;
-    return Math.min(Math.max(limit * SUPERSEDED_OVERFETCH, limit), SUPERSEDED_OVERFETCH_CAP);
-}
-export async function searchKnowledge(query, opts) {
-    const bridge = await getBridge();
-    if (!bridge)
-        return [];
-    const scope = opts?.scope ?? 'shared';
-    const limit = opts?.limit ?? 10;
-    const minScore = opts?.minScore ?? 0.3;
-    const store = opts?.store ?? 'all';
-    const targets = [];
-    if (store !== 'global') {
-        targets.push({
-            ns: namespace(scope),
-            root: opts?.rootDir ?? getProjectRoot(),
-            label: scope,
-            boost: PROJECT_SCOPE_BOOST,
-        });
-    }
-    if (store !== 'project') {
-        targets.push({
-            ns: namespace('global'),
-            dbPath: GLOBAL_BRAIN_SENTINEL,
-            root: globalBrainRoot(),
-            label: 'global',
-            boost: 0,
-        });
-    }
-    const includeSuperseded = opts?.includeSuperseded === true;
-    const perTarget = await Promise.all(targets.map(async (t) => {
-        const meta = readMetadata(t.root);
-        const hasMeta = hasKnowledgeMetadata(t.root);
-        const live = new Set();
-        for (const m of meta)
-            if (m.contentHash)
-                live.add(m.contentHash);
-        // Old versions dominate a long-lived store, so a 1:1 fetch would come back
-        // nearly empty once they are filtered out. Over-fetch, then trim.
-        const fetchLimit = includeSuperseded ? limit : supersededOverfetchLimit(limit, live);
-        const result = await bridge
-            .bridgeSearchEntries({
-            query,
-            namespace: t.ns,
-            limit: fetchLimit,
-            threshold: minScore,
-            dbPath: t.dbPath,
-            skipRerank: opts?.skipRerank,
-            includeSuperseded,
-            rootDir: t.root,
-        })
-            .catch(() => null);
-        if (!result?.success || !result.results.length)
-            return [];
-        const hashToFile = new Map();
-        for (const m of meta)
-            hashToFile.set(m.contentHash, m.filePath);
-        const kept = includeSuperseded
-            ? result.results
-            : result.results.filter((r) => !isSupersededKey(String(r.key ?? ''), live, hasMeta));
-        return kept.slice(0, limit).map((r) => {
-            const parts = r.key.startsWith('doc:') ? r.key.split(':') : [];
-            const hash = parts[1] ?? '';
-            const idx = parseInt(parts[2] ?? '0', 10);
-            // The src: tag stored at ingest is the chunk's OWN provenance — the
-            // hash→file map can misattribute when two documents share identical
-            // content, and goes empty when a re-ingested file's hash changed.
-            const srcTag = (r.tags ?? []).find((tag) => tag.startsWith('src:'));
-            const superseded = includeSuperseded && isSupersededKey(String(r.key ?? ''), live, hasMeta);
-            return {
-                id: r.id,
-                filePath: srcTag ? srcTag.slice(4) : (hashToFile.get(hash) ?? ''),
-                // Serve the head of the chunk only — chunks are heading-anchored, so the
-                // head carries the most relevant text, and full chunks (up to ~3.2K
-                // chars) bloat every search response.
-                text: typeof r.content === 'string' && r.content.length > SEARCH_EXCERPT_TEXT_CAP
-                    ? r.content.slice(0, SEARCH_EXCERPT_TEXT_CAP)
-                    : r.content,
-                similarity: r.score + t.boost,
-                chunkIndex: Number.isNaN(idx) ? 0 : idx,
-                scope: t.label,
-                ...(superseded ? { superseded: true } : {}),
-            };
-        });
-    }));
-    return perTarget
-        .flat()
-        .sort((a, b) => b.similarity - a.similarity)
-        .slice(0, limit);
-}
-// ── List / Remove ──────────────────────────────────────────────────
-export function listDocuments(rootDir = getProjectRoot(), scope) {
-    const all = readMetadata(rootDir);
-    return scope ? all.filter((m) => m.scope === scope) : all;
-}
-export async function removeDocument(filePath, scope = 'shared', rootDir = getProjectRoot()) {
-    removeMetadataEntry(rootDir, path.resolve(filePath), scope);
-    // SQLite cleanup: bridge doesn't expose delete-by-key, so metadata removal is sufficient.
-    // Orphaned SQLite entries get swept on next full re-index or TTL expiry.
-}
-// ── Filesystem reconciliation (item 4b-i) ──────────────────────────
-/**
- * True for macOS AppleDouble sidecars (`._name`).
- *
- * Matches on the BASENAME PREFIX only. A legitimate document may contain `._`
- * elsewhere in its name (`v1._2-release.md`), or live under a dot-directory
- * that is deliberately indexed (`.monodesign/` critique snapshots), and
- * neither may be rejected.
- */
-export function isResourceFork(filePath) {
-    return path.basename(filePath).startsWith('._');
-}
-/**
- * Reconcile the document index against the filesystem: find index entries whose
- * source file no longer exists and, only when explicitly asked, tombstone them.
- *
- * WHY — `removeDocument` only ever tombstoned metadata, and nothing has ever
- * compared the index against the disk, so a deleted file stayed searchable
- * forever. Measured 2026-07-28: 109 of 257 live entries (42.4%) had no file
- * behind them, including `docs/concepts/memory.md`. The Second Brain was
- * answering questions from documents the user had deleted.
- *
- * WHY IT IS THIS CAUTIOUS — "drop the index entry when the file is missing" is
- * a rule with a known catastrophic reading. A missing file is also an unmounted
- * volume, a checked-out branch, a partial clone, or a permissions failure. Two
- * guards were tried against real data and REJECTED; they are recorded here so
- * they are not re-proposed:
- *
- *   - "abort if >50% of entries are missing" — the real, legitimate missing
- *     fraction was 42.4%, so the threshold never fires in the one case we have.
- *     Any threshold that would have blocked this reconcile is fitted to nothing.
- *   - "only reconcile when the parent directory still exists" — 26 of the 109
- *     missing files had no parent directory, because `docs/concepts`,
- *     `docs/adrs` and `docs/commands` were legitimately deleted wholesale. A
- *     deleted directory and an unmounted volume are indistinguishable there.
- *
- * What does discriminate is the ROOT. An intact, readable root carrying a
- * metadata log means the tree is genuinely present, so a missing file is
- * genuinely gone. A missing root means nothing beneath it is knowable and
- * nothing may be removed — hence throw rather than reconcile.
- *
- * Removal tombstones metadata; it does not delete store rows. Chunks stay on
- * disk and fall out of search through the existing superseded filter, which
- * keeps this consistent with the mark-don't-destroy rule and leaves the whole
- * operation reversible from the archive.
- */
-export async function reconcileIndex(rootDir = getProjectRoot(), opts) {
-    const apply = opts?.apply === true;
-    // Root guard — the unmounted-volume case. Every file below a missing root
-    // looks deleted, so this must abort rather than reconcile.
-    if (!rootDir || !fs.existsSync(rootDir)) {
-        throw new Error(`reconcileIndex: project root does not exist: ${rootDir} — refusing to reconcile ` +
-            `(an unmounted volume makes every indexed file look deleted)`);
-    }
-    if (!hasKnowledgeMetadata(rootDir)) {
-        throw new Error(`reconcileIndex: no knowledge metadata log under ${rootDir} — refusing to reconcile ` +
-            `("no metadata" must not read as "everything is stale")`);
-    }
-    const records = readMetadata(rootDir).filter((m) => !opts?.scope || m.scope === opts.scope);
-    const missing = records.filter((m) => !fs.existsSync(m.filePath));
-    if (!apply || missing.length === 0) {
-        return { missing, scanned: records.length, applied: apply, removed: 0 };
-    }
-    // Archive BEFORE removing, inside the operation so no caller can bypass it
-    // by forgetting — the same precondition rule the delete path uses.
-    const dir = path.join(rootDir, '.monomind', 'knowledge', 'archive');
-    fs.mkdirSync(dir, { recursive: true });
-    const stamp = new Date().toISOString().replace(/[:.]/g, '-');
-    const archivePath = path.join(dir, `reconcile-${stamp}.jsonl`);
-    fs.writeFileSync(archivePath, `${missing.map((m) => JSON.stringify(m)).join('\n')}\n`, 'utf-8');
-    let removed = 0;
-    for (const m of missing) {
-        removeMetadataEntry(rootDir, m.filePath, m.scope);
-        removed++;
-    }
-    return { missing, scanned: records.length, applied: true, removed, archivePath };
-}
-// ── OKF Export ─────────────────────────────────────────────────────
-export async function exportToOKF(outputDir, rootDir = getProjectRoot(), scope = 'shared') {
-    const docs = listDocuments(rootDir, scope);
-    fs.mkdirSync(outputDir, { recursive: true });
-    let exported = 0;
-    const indexEntries = [];
-    for (const doc of docs) {
-        // Read original content
-        let content = '';
-        try {
-            if (fs.existsSync(doc.filePath)) {
-                const entry = toFileEntry(doc.filePath);
-                content = await extractText(entry);
-            }
-        }
-        catch {
-            continue;
-        }
-        if (!content)
-            continue;
-        const title = path.basename(doc.filePath, path.extname(doc.filePath));
-        const ext = path.extname(doc.filePath).toLowerCase();
-        const relativePath = path.relative(rootDir, doc.filePath);
-        const slug = title.replace(/[^a-zA-Z0-9._-]+/g, '-').toLowerCase();
-        const outFile = path.join(outputDir, `${slug}.md`);
-        const yamlEscape = (s) => /[:"'[\]{}#&*!|>%@`]/.test(s) ? `"${s.replace(/\\/g, '\\\\').replace(/"/g, '\\"')}"` : s;
-        const frontmatter = [
-            '---',
-            `type: Document`,
-            `title: ${yamlEscape(title)}`,
-            `description: ${yamlEscape(`Extracted from ${path.basename(doc.filePath)}`)}`,
-            `resource: ${yamlEscape(relativePath)}`,
-            `tags: ["document", ${yamlEscape(ext.slice(1))}]`,
-            `timestamp: ${yamlEscape(doc.indexedAt)}`,
-            `contentHash: ${yamlEscape(doc.contentHash)}`,
-            `chunkCount: ${doc.chunkCount}`,
-            '---',
-            '',
-        ].join('\n');
-        fs.writeFileSync(outFile, frontmatter + content, 'utf-8');
-        indexEntries.push(`* [${title}](${slug}.md) - ${path.basename(doc.filePath)} (${doc.chunkCount} chunks)`);
-        exported++;
-    }
-    // Write index.md
-    const indexContent = [
-        `# Knowledge Bundle`,
-        '',
-        `Exported from monomind on ${new Date().toISOString().slice(0, 10)}`,
-        '',
-        ...indexEntries,
-        '',
-    ].join('\n');
-    fs.writeFileSync(path.join(outputDir, 'index.md'), indexContent, 'utf-8');
-    return { exported, outputDir };
-}
-// ── OKF Import ─────────────────────────────────────────────────────
-export async function importFromOKF(bundleDir, scope = 'shared', rootDir = getProjectRoot()) {
-    const resolved = path.resolve(bundleDir);
-    const files = fs
-        .readdirSync(resolved)
-        .filter((f) => f.endsWith('.md') && f !== 'index.md' && f !== 'log.md')
-        .map((f) => path.join(resolved, f));
-    const result = {
-        filesProcessed: 0,
-        filesSkipped: 0,
-        totalChunks: 0,
-        errors: [],
-        results: [],
-    };
-    for (const file of files) {
-        const r = await ingestDocument(file, scope, rootDir);
-        result.results.push(r);
-        if (r.skipped) {
-            result.filesSkipped++;
-        }
-        else {
-            result.filesProcessed++;
-            result.totalChunks += r.chunksIndexed;
-        }
-        if (r.error && !r.skipped)
-            result.errors.push(`${r.filePath}: ${r.error}`);
-    }
-    return result;
-}
+export { chunkSpans } from './document-chunking.js';
+export { findDocumentRecord, hasKnowledgeMetadata, isResourceFork, isSupersededKey, listDocuments, listDocumentVersions, liveContentHashes, reconcileIndex, removeDocument, supersededOverfetchLimit, } from './document-index.js';
+export { ingestDirectory, ingestDocument } from './document-ingest.js';
+export { searchKnowledge } from './document-search.js';
+export { getKnowledgeRoot } from './document-store.js';
+export { exportToOKF, importFromOKF } from './okf-bundle.js';
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