agent-nuvira 3.3.13 → 3.3.15

package/dist/learning/knowledge-base.js

@@ -15,6 +15,22 @@
  * vector namespace (`knowledge-<tag>`), so tags never bleed into each other and
  * a tag can be forgotten without touching anything else.
  *
+ * Retrieval is relevance-FLOORED (`DEFAULT_KNOWLEDGE_MIN_SIMILARITY`), because
+ * "the nearest k neighbours" is not the same claim as "k relevant passages":
+ * an unrelated question must be able to come back empty rather than receive the
+ * closest six chunks of a document it has nothing to do with.
+ *
+ * Retrieval is also HYBRID (Phase 2.2–2.4): a dense (vector) half and a lexical
+ * (BM25, see `lexical-search.ts`) half are fused with Reciprocal Rank Fusion and
+ * then capped per source document. The two halves fail on different questions —
+ * embeddings miss the exact identifier, clause number or error code a user pastes
+ * in, and BM25 misses a paraphrase with no shared words — so ranking both and
+ * fusing their RANKS (not their incomparable scores) gets both. The cosine floor
+ * still governs DENSE evidence; lexical evidence is governed by its own term
+ * overlap, which is why an unrelated question (no shared vocabulary) still comes
+ * back empty from both halves. `fusion: 'dense'` reproduces vector-only
+ * retrieval for a caller that wants it or for the eval to compare against.
+ *
  * The retrieved chunks are USER DATA; the model supplies the generic half of an
  * answer (and `web-research` supplies the net-based half). `formatKnowledgeContext`
  * labels each chunk with its source file so the model can attribute precisely
@@ -25,12 +41,15 @@
  * listing/removal. Everything lives in the Nuvira data dir (`~/.nuvira/memory`),
  * never in a repository or package.
  */
-import { existsSync, mkdirSync, readFileSync, readdirSync, statSync, writeFileSync } from 'node:fs';
-import { join, extname, basename } from 'node:path';
+import { existsSync, mkdirSync, readFileSync, readdirSync, rmSync, statSync, unlinkSync, writeFileSync } from 'node:fs';
+import { createHash } from 'node:crypto';
+import { join, extname, basename, relative, isAbsolute } from 'node:path';
 import { envBuff, resolveNuviraHome } from '../config/paths.js';
 import { embed, RETRIEVAL_MODEL } from '../memory/embedder.js';
-import { getVectorStore } from '../memory/vector-store.js';
-import { chunkText, DEFAULT_CHUNK_TOKENS, DEFAULT_OVERLAP_TOKENS } from './retrieval.js';
+import { getVectorStore, cosineSimilarity } from '../memory/vector-store.js';
+import { DEFAULT_CHUNK_TOKENS, DEFAULT_OVERLAP_TOKENS } from './retrieval.js';
+import { chunkMarkdown, parseMarkdownOutline } from './markdown-outline.js';
+import { bm25Search } from './lexical-search.js';
 import { logger } from '../utils/logger.js';
 // ─── Constants ──────────────────────────────────────────────────────────────
 /** A tag is a sandboxed namespace segment: lowercase alphanumerics + hyphens, with at least one alphanumeric. */
@@ -41,6 +60,70 @@ export const KNOWLEDGE_NAMESPACE_PREFIX = 'knowledge-';
 export const KNOWLEDGE_MANIFEST_FILE = 'knowledge-index.json';
 /** Default chunks returned per query. */
 export const DEFAULT_KNOWLEDGE_TOP_K = 6;
+/**
+ * Relevance floor for retrieval.
+ *
+ * Every backend scores in cosine similarity, where 1 means "the same direction"
+ * and 0 means "unrelated", so a hit below this is at best a weak topic touch.
+ * The floor is what makes an HONEST empty answer reachable: nearest-neighbour
+ * search always returns its k nearest neighbours, so without a floor the k-th
+ * can be a passage about something else entirely and an unrelated question still
+ * receives a confident-looking block of the wrong document. A hit below the
+ * floor is not evidence about the question, so it is dropped here rather than
+ * left to the model to notice and ignore.
+ *
+ * CALIBRATED, NOT GUESSED. Cosine similarity between a question and its own
+ * document is a property of the EMBEDDING MODEL, so this number only means
+ * anything next to the model that produced the vectors. On the eval corpus with
+ * the retrieval model (`RETRIEVAL_MODEL`, bge-small-en-v1.5), unrelated
+ * questions reach up to 0.425 and the lowest-scoring CORRECT answer sits at
+ * 0.635 (p50 0.772). 0.5 is the round value inside that
+ * measured gap with margin on both sides: above every leak probe and below every
+ * correct answer. `tests/live/knowledge-eval-live.test.ts` prints the band and
+ * FAILS if the shipped floor falls outside it, so this is re-measurable rather
+ * than folklore.
+ *
+ * IT IS TIER-SPECIFIC, and the embedder is TIERED. If the local ONNX model
+ * cannot load, `embed` falls back to a different model — Python
+ * `all-MiniLM-L6-v2`, on a different similarity scale — or to a zero vector,
+ * WITHOUT throwing. A floor calibrated for one model is simply wrong for
+ * another, and wrong in a way that looks measured. The live eval therefore proves
+ * which model actually ran (an identity probe) before it reports a band, and
+ * fails loudly if they disagree. The offline eval uses its OWN floor and says so
+ * (`KNOWLEDGE_EVAL_OFFLINE_MIN_SIMILARITY`), because a bag-of-words vectorizer is
+ * not on this model's scale at all.
+ */
+export const DEFAULT_KNOWLEDGE_MIN_SIMILARITY = 0.5;
+/**
+ * How many chunks ONE source document may contribute to a result.
+ *
+ * Fusion alone can hand the whole top-k to whichever document the query happens
+ * to touch most, because a long document has more chances to contain a term —
+ * so a single highly-ranked file would crowd out the shorter document that
+ * actually answers the question. The cap promotes diversity of SOURCES.
+ *
+ * It is deliberately relaxed to "no cap" when the candidate pool has only one
+ * source: the common case is a tag holding a single document, and capping it
+ * there would throw away half the passages for no diversity to gain.
+ */
+export const DEFAULT_KNOWLEDGE_MAX_PER_SOURCE = 3;
+/**
+ * Dense AND lexical candidates considered before fusion, as a multiple of topK
+ * (floored at MIN_CANDIDATE_POOL). Fusion has to see more than `topK` from each
+ * half: a passage the dense half ranked 12th and the lexical half ranked 2nd
+ * should be able to win, and it can only do that if both halves were given a
+ * pool deeper than the answer.
+ */
+const CANDIDATE_POOL_MULTIPLIER = 4;
+const MIN_CANDIDATE_POOL = 24;
+/**
+ * Reciprocal Rank Fusion's rank constant (Cormack et al., 2009). A larger value
+ * flattens the difference between adjacent ranks. 60 is the standard default and
+ * is what makes RRF safe here: it fuses RANKS, so cosine similarity — which is
+ * on the embedding model's scale — is never added to a BM25 score, which is on
+ * its own unbounded scale. The two numbers are never compared, only their orders.
+ */
+const RRF_K = 60;
 /** Directories never walked when a tag is pointed at a folder. */
 const IGNORE_DIRS = new Set([
     'node_modules', '.git', 'dist', 'build', '.next', '.cache', '.venv', 'venv',
@@ -116,6 +199,70 @@ export function getKnowledgeTag(tag) {
     const normalized = normalizeKnowledgeTag(tag);
     return readKnowledgeManifest().tags[normalized] ?? null;
 }
+// ─── Document store (the extracted text, kept so a section can be READ) ─────
+//
+// Retrieval returns passages, but "implement this spec" needs the section as the
+// author wrote it — in order, complete, quotable. Re-extracting on every read
+// would be slow and, for a PDF, would mean re-running the whole extractor just
+// to show one heading's worth of text, so the extracted text is stored beside the
+// vectors. It is user data in the same data dir, and it is removed with the tag.
+/** SHA-1 of the extracted text — the change detector, not a security control. */
+function contentHashOf(text) {
+    return createHash('sha1').update(text).digest('hex');
+}
+/** Stable id for a document, derived from its path. */
+export function documentIdFor(sourcePath) {
+    return createHash('sha1').update(sourcePath).digest('hex').slice(0, 16);
+}
+/** A document's display title: its first heading, or its basename. */
+function documentTitleOf(text, sourcePath) {
+    try {
+        const first = parseMarkdownOutline(text)[0];
+        if (first && first.level > 0)
+            return first.title;
+    }
+    catch {
+        // Fall through to the basename — a title is never worth failing an ingest.
+    }
+    return basename(sourcePath);
+}
+function documentStoreDir(tag) {
+    return join(memoryDir(), 'knowledge-docs', normalizeKnowledgeTag(tag));
+}
+function documentStorePath(tag, docId) {
+    return join(documentStoreDir(tag), `${docId}.txt`);
+}
+/** Persist a document's extracted text. Best-effort — vectors remain the truth. */
+function writeStoredDocument(tag, docId, text) {
+    try {
+        const dir = documentStoreDir(tag);
+        if (!existsSync(dir))
+            mkdirSync(dir, { recursive: true });
+        writeFileSync(documentStorePath(tag, docId), text, 'utf-8');
+    }
+    catch {
+        // A failed write costs a later read, never an ingest.
+    }
+}
+function readStoredDocument(tag, docId) {
+    try {
+        const path = documentStorePath(tag, docId);
+        return existsSync(path) ? readFileSync(path, 'utf-8') : null;
+    }
+    catch {
+        return null;
+    }
+}
+function deleteStoredDocument(tag, docId) {
+    try {
+        const path = documentStorePath(tag, docId);
+        if (existsSync(path))
+            unlinkSync(path);
+    }
+    catch {
+        // Best-effort — an orphaned text file is inert (nothing references it).
+    }
+}
 // ─── File collection ────────────────────────────────────────────────────────
 /** Recursively collect files under a path (bounded, ignores build/vendor dirs). */
 export function collectKnowledgeFiles(root, out = [], depth = 0) {
@@ -186,22 +333,37 @@ async function extractFileText(filePath) {
  * so re-ingesting a changed document overwrites its chunks rather than
  * duplicating them.
  */
-export async function ingestKnowledgeText(tag, sourcePath, text, opts = {}) {
+export async function ingestKnowledgeText(tag, sourcePath, text, opts = {}, 
+/**
+ * How many chunks this same `<tag>:<sourcePath>` contributed LAST time, so a
+ * document that got shorter has its retired tail removed. `ingestKnowledge`
+ * passes the count it reads from the manifest.
+ */
+previousChunkCount = 0) {
     const normalized = normalizeKnowledgeTag(tag);
     const chunkTokens = opts.chunkTokens ?? DEFAULT_CHUNK_TOKENS;
     const overlapTokens = opts.overlapTokens ?? DEFAULT_OVERLAP_TOKENS;
     const embedFn = opts.embedFn ?? ((t) => embed(t, undefined, false, RETRIEVAL_MODEL));
     const label = `${normalized}:${sourcePath}`;
-    const chunks = chunkText(text, label, chunkTokens, overlapTokens);
+    // Structure-aware: each chunk is tagged with the heading chain it sits under,
+    // and is EMBEDDED with that chain prepended (see markdown-outline.ts) while the
+    // stored/quotable text stays exactly as it appears in the document.
+    const chunks = chunkMarkdown(text, label, chunkTokens, overlapTokens);
     const store = getVectorStore(namespaceForTag(normalized));
+    let stored = 0;
     for (const chunk of chunks) {
         let vector;
         try {
-            vector = await embedFn(chunk.text);
+            vector = await embedFn(chunk.embedText);
         }
         catch {
-            // A failed embed leaves a zero vector (never outranks a real match).
-            vector = new Array(384).fill(0);
+            // SKIP the chunk — never store a placeholder. A zero vector was inserted
+            // here before: it scores 0 (cosine guards the zero magnitude) so it could
+            // never win a search, but it cost a scan forever and it made a partially
+            // indexed document read as fully indexed. A hole the caller is TOLD about
+            // beats a dead entry nobody can see.
+            opts.onChunkSkipped?.(`chunk ${chunk.chunkIndex + 1} of ${basename(sourcePath)}`);
+            continue;
         }
         await store.insert(chunk.id, vector, {
             kind: 'knowledge-chunk',
@@ -209,10 +371,26 @@ export async function ingestKnowledgeText(tag, sourcePath, text, opts = {}) {
             sourcePath,
             chunkIndex: chunk.chunkIndex,
             text: chunk.text,
+            headingPath: chunk.headingPath,
+            title: chunk.title,
             tokenCount: chunk.tokenCount,
         });
+        stored += 1;
     }
-    return chunks.length;
+    // A document that got SHORTER must not leave its old tail behind. Chunk ids
+    // are `<tag>:<path>#<i>` and `insert` overwrites only the indices the new
+    // version produced, so the retired chunks would otherwise stay in the
+    // namespace and keep being retrieved for the life of the tag.
+    for (let i = chunks.length; i < previousChunkCount; i += 1) {
+        try {
+            await store.delete(`${label}#${i}`);
+        }
+        catch {
+            // Best-effort: a failed delete leaves one stale chunk, which the relevance
+            // floor may still drop — but it must never break the ingest.
+        }
+    }
+    return stored;
 }
 /**
  * Ingest one or more files/directories under a tag. Extraction, chunking and
@@ -223,7 +401,7 @@ export async function ingestKnowledge(tag, paths, opts = {}) {
     if (!isValidKnowledgeTag(normalized)) {
         throw new Error(`Invalid knowledge tag '${tag}' — it must contain at least one letter or digit.`);
     }
-    const result = { tag: normalized, files: 0, chunks: 0, skipped: [] };
+    const result = { tag: normalized, files: 0, chunks: 0, unchanged: 0, skipped: [] };
     const manifest = readKnowledgeManifest();
     const entry = manifest.tags[normalized] ?? {
         tag: normalized,
@@ -248,16 +426,56 @@ export async function ingestKnowledge(tag, paths, opts = {}) {
             continue;
         }
         try {
-            const chunks = await ingestKnowledgeText(normalized, file, extracted.text, opts);
+            // The document's previous contribution, read BEFORE the write — it drives
+            // the retired-tail delete, the recorded count and the unchanged check.
+            const previous = entry.documents.find((d) => d.path === file);
+            const docId = documentIdFor(file);
+            const contentHash = contentHashOf(extracted.text);
+            // UNCHANGED: same text as last time. Re-embedding it would cost the whole
+            // document again to arrive at byte-identical vectors, so the stored text is
+            // refreshed (cheap, and it is what a section read serves) and the vectors
+            // are left alone.
+            if (previous && previous.contentHash === contentHash) {
+                writeStoredDocument(normalized, docId, extracted.text);
+                result.unchanged += 1;
+                continue;
+            }
+            let embedFailures = 0;
+            const chunks = await ingestKnowledgeText(normalized, file, extracted.text, { ...opts, onChunkSkipped: () => { embedFailures += 1; } }, previous?.chunks ?? 0);
+            if (chunks === 0) {
+                // Every chunk failed to embed. Recording the document would claim a file
+                // that contributes nothing and reads as indexed; say what happened.
+                result.skipped.push({ path: file, reason: 'no chunk could be embedded — nothing was indexed' });
+                continue;
+            }
             result.files += 1;
             result.chunks += chunks;
+            if (embedFailures > 0) {
+                result.skipped.push({
+                    path: file,
+                    reason: `${embedFailures} chunk(s) could not be embedded and were not indexed`,
+                });
+            }
+            // The extracted text is kept so a section can be read verbatim later;
+            // recorded BEFORE the manifest write so a crash cannot leave a document
+            // recorded with no readable text behind it.
+            writeStoredDocument(normalized, docId, extracted.text);
             // Re-ingesting a changed document replaces its chunks; keep the recorded
             // count in step by subtracting the previous contribution first.
-            const previous = entry.documents.find((d) => d.path === file);
-            if (previous)
+            if (previous) {
                 entry.chunkCount -= previous.chunks;
+                if (previous.docId !== docId)
+                    deleteStoredDocument(normalized, previous.docId);
+            }
             entry.documents = entry.documents.filter((d) => d.path !== file);
-            entry.documents.push({ path: file, chunks, addedAt: Date.now() });
+            entry.documents.push({
+                docId,
+                path: file,
+                title: documentTitleOf(extracted.text, file),
+                chunks,
+                addedAt: Date.now(),
+                contentHash,
+            });
             entry.chunkCount += chunks;
         }
         catch (err) {
@@ -265,28 +483,134 @@ export async function ingestKnowledge(tag, paths, opts = {}) {
         }
     }
     entry.updatedAt = Date.now();
-    manifest.tags[normalized] = entry;
-    writeKnowledgeManifest(manifest);
+    // A tag that ingested nothing AND had nothing before is not a tag: recording
+    // it would put an empty entry in `list` (and in the model's view of what the
+    // user has), which reads as "this document set exists" when nothing was
+    // indexed at all.
+    if (entry.documents.length > 0 || manifest.tags[normalized]) {
+        manifest.tags[normalized] = entry;
+        writeKnowledgeManifest(manifest);
+    }
     return result;
 }
-// ─── Query ──────────────────────────────────────────────────────────────────
-/** Embed the question and return the tag's top-k chunks. Never throws. */
+/** The source document a stored chunk belongs to (its path, else its id). */
+function sourcePathOf(entry) {
+    return String(entry.metadata?.sourcePath ?? entry.id);
+}
+/**
+ * Embed the question and return the tag's top-k chunks. Never throws.
+ *
+ * Two retrievers run over the same namespace and their RANKS are fused:
+ *
+ *   1. **Dense** — cosine over the stored vectors, gated by `minSimilarity`.
+ *      This is the Phase-0 relevance floor and it is unchanged: a passage the
+ *      embeddings do not consider related is not dense evidence.
+ *   2. **Lexical** — BM25 over the stored chunk text, which can find the exact
+ *      term a dense retriever missed. A lexical hit is evidence by itself, so it
+ *      is admitted even when its cosine sits below the floor — that is the whole
+ *      reason the second retriever exists, and it is why `minSimilarity` alone
+ *      can no longer force an empty result for a question that shares vocabulary
+ *      with the corpus. Pass `fusion: 'dense'` to get the old, purely-cosine
+ *      behaviour.
+ *
+ * Reciprocal Rank Fusion scores each candidate `Σ 1/(RRF_K + rank)`. Scores are
+ * never summed across halves — cosine and BM25 are on different scales, and
+ * adding them would silently weight whichever happens to have the larger range.
+ * RRF only needs each half to ORDER its candidates, so a backend change cannot
+ * move the fusion.
+ *
+ * The fused ranking is then capped per source document, so one long file cannot
+ * take every slot from the shorter one that answers the question.
+ */
 export async function queryKnowledge(tag, question, opts = {}) {
     const normalized = normalizeKnowledgeTag(tag);
     const topK = opts.topK ?? DEFAULT_KNOWLEDGE_TOP_K;
+    const minSimilarity = opts.minSimilarity ?? DEFAULT_KNOWLEDGE_MIN_SIMILARITY;
+    const fusion = opts.fusion ?? 'hybrid';
+    const minLexicalScore = opts.minLexicalScore ?? 0;
+    const maxPerSource = opts.maxPerSource ?? DEFAULT_KNOWLEDGE_MAX_PER_SOURCE;
     const embedFn = opts.embedFn ?? ((t) => embed(t, undefined, false, RETRIEVAL_MODEL));
     try {
         const queryVector = await embedFn(question);
         const store = getVectorStore(namespaceForTag(normalized));
-        const results = await store.search(queryVector, topK, (entry) => {
-            return entry.metadata?.kind === 'knowledge-chunk' && entry.metadata?.tag === normalized;
-        });
-        return results.map(({ entry, similarity }) => ({
+        const scoped = (entry) => entry.metadata?.kind === 'knowledge-chunk' && entry.metadata?.tag === normalized;
+        const candidateK = Math.max(topK * CANDIDATE_POOL_MULTIPLIER, MIN_CANDIDATE_POOL);
+        const denseResults = await store.search(queryVector, candidateK, scoped);
+        // Dense evidence, floored. A non-finite score is treated as a miss: it must
+        // never compare as "relevant".
+        const denseKept = denseResults.filter(({ similarity }) => Number.isFinite(similarity) && similarity >= minSimilarity);
+        if (denseKept.length < denseResults.length) {
+            logger.debug(`Knowledge query for '${normalized}' dropped ${denseResults.length - denseKept.length} hit(s) below the ${minSimilarity} relevance floor.`);
+        }
+        const byId = new Map();
+        for (const { entry } of denseResults)
+            byId.set(entry.id, entry);
+        const candidates = new Map();
+        const fuse = (entry, similarity, fromDense, rank) => {
+            const contribution = 1 / (RRF_K + rank + 1);
+            const existing = candidates.get(entry.id);
+            if (existing) {
+                existing.rrf += contribution;
+                existing.fromDense = existing.fromDense || fromDense;
+            }
+            else {
+                candidates.set(entry.id, { entry, similarity, fromDense, rrf: contribution });
+            }
+        };
+        // Dense first, so a passage found by BOTH keeps the backend's similarity
+        // rather than the locally recomputed one.
+        denseKept.forEach(({ entry, similarity }, rank) => fuse(entry, similarity, true, rank));
+        if (fusion === 'hybrid') {
+            // Lexical over EVERY scoped chunk, not just the dense pool: a passage the
+            // dense half never ranked is exactly the one BM25 is here to find.
+            // Rebuilt per query on purpose — see lexical-search.ts, no index to drift.
+            const documents = [];
+            for (const entry of await store.getAll()) {
+                if (!scoped(entry))
+                    continue;
+                byId.set(entry.id, entry);
+                documents.push({ id: entry.id, text: String(entry.metadata?.text ?? '') });
+            }
+            const lexicalHits = bm25Search(documents, question, candidateK).filter((h) => h.score >= minLexicalScore);
+            lexicalHits.forEach((hit, rank) => {
+                const entry = byId.get(hit.id);
+                if (!entry)
+                    return;
+                // The similarity is kept for the citation even when it is below the
+                // floor — reporting it is what lets a reader see that this passage came
+                // from a term match rather than a near neighbour.
+                fuse(entry, cosineSimilarity(queryVector, entry.vector), false, rank);
+            });
+        }
+        if (candidates.size === 0)
+            return [];
+        // Deterministic order: RRF desc, then id — so equal scores never depend on
+        // Map insertion order, which is what keeps the eval reproducible.
+        const ranked = [...candidates.values()].sort((a, b) => b.rrf - a.rrf || a.entry.id.localeCompare(b.entry.id));
+        // Diversity cap. Only meaningful when there IS more than one source to
+        // promote, so a single-document tag (the common case) is never truncated.
+        const sources = new Set(ranked.map((c) => sourcePathOf(c.entry)));
+        const cap = sources.size > 1 ? maxPerSource : topK;
+        const perSource = new Map();
+        const selected = [];
+        for (const candidate of ranked) {
+            const source = sourcePathOf(candidate.entry);
+            const used = perSource.get(source) ?? 0;
+            if (used >= cap)
+                continue;
+            perSource.set(source, used + 1);
+            selected.push(candidate);
+            if (selected.length >= topK)
+                break;
+        }
+        return selected.map(({ entry, similarity, fromDense }) => ({
             tag: normalized,
             text: String(entry.metadata?.text ?? ''),
-            sourcePath: String(entry.metadata?.sourcePath ?? entry.id),
+            sourcePath: sourcePathOf(entry),
             chunkIndex: Number(entry.metadata?.chunkIndex ?? 0),
             similarity,
+            headingPath: entry.metadata?.headingPath ? String(entry.metadata.headingPath) : undefined,
+            evidence: fromDense ? 'dense' : 'term',
         }));
     }
     catch (err) {
@@ -295,6 +619,152 @@ export async function queryKnowledge(tag, question, opts = {}) {
     }
 }
 // ─── Forget ─────────────────────────────────────────────────────────────────
+// ─── Reading a document, whole or by section ────────────────────────────────
+//
+// Retrieval answers "where is it mentioned"; this answers "what does it say",
+// in the document's own order and wording. The two are different jobs: a
+// spec-driven build needs the section verbatim, not the six most similar
+// paragraphs of it, and no amount of chunk ranking substitutes for that.
+/** Cap on a read, so "the whole document" cannot become an unbounded prompt. */
+export const MAX_READ_CHARS = 40_000;
+/**
+ * Find the document a caller means. Accepts a docId, an exact path, or a
+ * basename; a basename that matches more than one document is reported as
+ * ambiguous rather than resolved by guessing, because guessing picks the wrong
+ * document silently, which is the failure this whole module is against.
+ */
+function resolveDocument(tag, docRef) {
+    const entry = getKnowledgeTag(tag);
+    if (!entry)
+        return { ok: false, reason: `No knowledge tag '${normalizeKnowledgeTag(tag)}' found.` };
+    const ref = docRef.trim();
+    const exact = entry.documents.find((d) => d.docId === ref || d.path === ref);
+    if (exact)
+        return { ok: true, doc: exact };
+    const byName = entry.documents.filter((d) => basename(d.path).toLowerCase() === ref.toLowerCase());
+    if (byName.length === 1)
+        return { ok: true, doc: byName[0] };
+    if (byName.length > 1) {
+        return {
+            ok: false,
+            reason: `'${ref}' matches ${byName.length} documents under '${entry.tag}' — use the full path or the doc id: ${byName
+                .map((d) => d.docId)
+                .join(', ')}`,
+        };
+    }
+    const available = entry.documents.map((d) => basename(d.path)).join(', ');
+    return { ok: false, reason: `No document '${ref}' under '${entry.tag}'. Available: ${available || '(none)'}` };
+}
+/**
+ * Read a document's text, or one of its sections.
+ *
+ * `section` is matched against the section's heading path, case-insensitively,
+ * with or without the ancestors (`"Token refresh"` finds
+ * `Auth Design > Token refresh`, and so does the full path). An unknown section
+ * returns the available ones instead of the whole document, because silently
+ * answering a narrower question with everything is how a reader concludes the
+ * document says something it never said.
+ */
+export function readKnowledgeDocument(tag, docRef, section) {
+    const resolved = resolveDocument(tag, docRef);
+    if (!resolved.ok)
+        return resolved;
+    const doc = resolved.doc;
+    const full = readStoredDocument(normalizeKnowledgeTag(tag), doc.docId);
+    if (full === null) {
+        return {
+            ok: false,
+            reason: `The text of '${basename(doc.path)}' is not stored (it was ingested by an older version). Re-ingest it: action: add.`,
+        };
+    }
+    let text = full;
+    let headingPath;
+    if (section && section.trim()) {
+        const want = section.trim().toLowerCase();
+        const sections = parseMarkdownOutline(full);
+        const match = sections.find((s) => {
+            const own = s.title.toLowerCase();
+            const chain = s.headingPath ? `${s.headingPath} > ${s.title}`.toLowerCase() : own;
+            return own === want || chain === want || chain.endsWith(` > ${want}`);
+        });
+        if (!match) {
+            const list = sections
+                .filter((s) => s.level > 0)
+                .slice(0, 40)
+                .map((s) => (s.headingPath ? `${s.headingPath} > ${s.title}` : s.title))
+                .join('\n  ');
+            return { ok: false, reason: `No section '${section}' in '${basename(doc.path)}'. Sections:\n  ${list}` };
+        }
+        text = match.text;
+        headingPath = match.headingPath ? `${match.headingPath} > ${match.title}` : match.title;
+    }
+    const truncated = text.length > MAX_READ_CHARS;
+    return {
+        ok: true,
+        text: truncated ? text.slice(0, MAX_READ_CHARS) : text,
+        truncated,
+        path: doc.path,
+        headingPath,
+    };
+}
+/** Every document under a tag, with its heading tree. */
+export function listKnowledgeSections(tag, docRef) {
+    const entry = getKnowledgeTag(tag);
+    if (!entry)
+        return [];
+    const docs = docRef ? (() => {
+        const resolved = resolveDocument(tag, docRef);
+        return resolved.ok ? [resolved.doc] : [];
+    })() : entry.documents;
+    return docs.map((doc) => {
+        const text = readStoredDocument(entry.tag, doc.docId);
+        const sections = text
+            ? parseMarkdownOutline(text)
+                .filter((s) => s.level > 0)
+                .map((s) => ({
+                title: s.title,
+                headingPath: s.headingPath,
+                level: s.level,
+                chars: s.text.length,
+            }))
+            : [];
+        return { docId: doc.docId, path: doc.path, title: doc.title, chunks: doc.chunks, addedAt: doc.addedAt, sections };
+    });
+}
+/**
+ * Remove one document from a tag: its chunks, its stored text, its manifest row.
+ * Used by `syncKnowledgeTag` when a file is no longer present under a synced
+ * root, and by the CLI to drop a single document without forgetting the tag.
+ */
+export async function removeKnowledgeDocument(tag, docRef) {
+    const normalized = normalizeKnowledgeTag(tag);
+    const resolved = resolveDocument(normalized, docRef);
+    if (!resolved.ok)
+        return false;
+    const doc = resolved.doc;
+    const manifest = readKnowledgeManifest();
+    const entry = manifest.tags[normalized];
+    if (entry) {
+        entry.documents = entry.documents.filter((d) => d.path !== doc.path);
+        entry.chunkCount = Math.max(0, entry.chunkCount - doc.chunks);
+        entry.updatedAt = Date.now();
+        if (entry.documents.length === 0)
+            delete manifest.tags[normalized];
+        writeKnowledgeManifest(manifest);
+    }
+    const store = getVectorStore(namespaceForTag(normalized));
+    const label = `${normalized}:${doc.path}`;
+    for (let i = 0; i < doc.chunks; i += 1) {
+        try {
+            await store.delete(`${label}#${i}`);
+        }
+        catch {
+            // Best-effort — a stale chunk is floored at query time rather than fatal.
+        }
+    }
+    deleteStoredDocument(normalized, doc.docId);
+    return true;
+}
 /** Remove a tag's vectors and manifest entry. Returns true when something was removed. */
 export async function forgetKnowledgeTag(tag) {
     const normalized = normalizeKnowledgeTag(tag);
@@ -308,8 +778,104 @@ export async function forgetKnowledgeTag(tag) {
     catch {
         // Best-effort — the manifest entry is already gone.
     }
+    // The stored extracted text is user data too, and `forget` has to mean forget:
+    // leaving it behind would keep the documents on disk with nothing pointing at
+    // them, which is worse than either keeping or removing them.
+    try {
+        rmSync(documentStoreDir(normalized), { recursive: true, force: true });
+    }
+    catch {
+        // Best-effort.
+    }
     return existed;
 }
+// True when `child` is `root` itself or lives beneath it, on ANY platform.
+// Deliberately NOT a `startsWith(root + '/')` test: manifest paths carry the
+// native separator, so on Windows a hardcoded `/` prefix never matches — the
+// document looks like it belongs to no synced root and a deleted file is
+// silently never pruned, so it keeps being served. `path.relative` is native.
+function isUnderRoot(root, child) {
+    const rel = relative(root, child);
+    return rel === '' || (!rel.startsWith('..') && !isAbsolute(rel));
+}
+/**
+ * Bring a tag up to date with the folders it is kept in step with.
+ *
+ * This is `add` plus the two things a folder being kept in step needs: content
+ * hashes mean an unchanged file is not re-extracted, re-chunked or re-embedded,
+ * and a file that has DISAPPEARED stops being served.
+ *
+ * Removal is scoped to the roots the caller actually synced. Syncing `./specs`
+ * must not delete documents ingested from somewhere else, so a document is only
+ * pruned when it lives under one of the synced directories AND was absent from
+ * that directory's enumeration — a precise rule, rather than "anything not in
+ * this list", which would quietly empty a tag the first time it was called with
+ * the wrong path.
+ */
+export async function syncKnowledgeTag(tag, paths, opts = {}) {
+    const normalized = normalizeKnowledgeTag(tag);
+    const result = {
+        tag: normalized,
+        added: 0,
+        changed: 0,
+        unchanged: 0,
+        removed: [],
+        chunks: 0,
+        skipped: [],
+    };
+    const files = [];
+    const directoryRoots = [];
+    for (const path of paths) {
+        let stat;
+        try {
+            stat = statSync(path);
+        }
+        catch {
+            result.skipped.push({ path, reason: 'not found' });
+            continue;
+        }
+        if (stat.isDirectory()) {
+            directoryRoots.push(path);
+            collectKnowledgeFiles(path, files);
+        }
+        else {
+            files.push(path);
+        }
+    }
+    // Snapshot BEFORE the write: the difference between the two manifests is what
+    // "added/changed/unchanged" means, and it must not be inferred from a counter.
+    const before = new Map((getKnowledgeTag(normalized)?.documents ?? []).map((d) => [d.path, d]));
+    const enumerated = new Set(files);
+    const ingest = await ingestKnowledge(normalized, files, opts);
+    result.skipped = ingest.skipped;
+    result.chunks = ingest.chunks;
+    // Classify the files the CALLER synced — the enumerated set — by diffing the
+    // two manifests. A document that is about to be pruned must not be counted as
+    // "unchanged": it is removed, and counting it here would report a sync as
+    // having kept something it just deleted.
+    const after = new Map((getKnowledgeTag(normalized)?.documents ?? []).map((d) => [d.path, d]));
+    for (const path of enumerated) {
+        const current = after.get(path);
+        if (!current)
+            continue; // could not be ingested — it is already in `skipped`
+        const previous = before.get(path);
+        if (!previous)
+            result.added += 1;
+        else if (previous.contentHash !== current.contentHash)
+            result.changed += 1;
+        else
+            result.unchanged += 1;
+    }
+    for (const path of before.keys()) {
+        if (enumerated.has(path))
+            continue;
+        const underSyncedRoot = directoryRoots.some((root) => isUnderRoot(root, path));
+        if (underSyncedRoot && (await removeKnowledgeDocument(normalized, path))) {
+            result.removed.push(path);
+        }
+    }
+    return result;
+}
 // ─── Formatting for the model ───────────────────────────────────────────────
 /**
  * Render retrieved chunks as context that ATTRIBUTES each part to the user's
@@ -323,11 +889,23 @@ export function formatKnowledgeContext(tag, hits) {
     }
     const parts = hits.map((h) => {
         const name = basename(h.sourcePath);
-        return `--- [from your data: ${name} · chunk ${h.chunkIndex + 1} · sim ${h.similarity.toFixed(3)}] ---\n${h.text}`;
+        // The section is part of the citation: "clause 4" is not attributable
+        // without it, and a reader checking the quote needs to know where to look.
+        const section = h.headingPath ? ` · §${h.headingPath}` : '';
+        // A term-only passage is marked as such: its `sim` is below the floor by
+        // construction, and a bare low number next to USER DATA reads as a retrieval
+        // mistake rather than as "this is the passage that contains your term".
+        const evidence = h.evidence === 'term' ? ' · term match' : '';
+        return `--- [from your data: ${name} · chunk ${h.chunkIndex + 1}${section} · sim ${h.similarity.toFixed(3)}${evidence}] ---\n${h.text}`;
     });
     return [
         `Knowledge tag: ${normalized} (${hits.length} relevant chunk${hits.length === 1 ? '' : 's'} from the user's own data)`,
         'Treat the following as USER DATA — quote it for facts about the user. For general advice, combine it with your own knowledge and, when current guidance is needed, the web-research tool, and say which part is which.',
+        // Relevance is measured (see DEFAULT_KNOWLEDGE_MIN_SIMILARITY), but a floor
+        // is a heuristic — so the fallback is stated as a policy, not left to chance:
+        // passages that do not answer the question must be reported as insufficient
+        // rather than stretched to fit.
+        'If these passages do not answer the question, say so plainly and answer from your own knowledge — do not stretch them to fit, and never assert a fact about the user\'s data that is not in them.',
         '',
         ...parts,
     ].join('\n');