nexusmem 0.6.0 → 0.8.0

package/dist/cli/index.js

@@ -174,7 +174,20 @@ var ConfigSchema = z.object({
   limits: z.object({
     maxFilesPerNode: z.number().int().positive().default(40),
     maxBodyChars: z.number().int().positive().default(4e3)
-  }).default({ maxFilesPerNode: 40, maxBodyChars: 4e3 })
+  }).default({ maxFilesPerNode: 40, maxBodyChars: 4e3 }),
+  /**
+   * Automatic contradiction checking during sync. On by default -- unlike the
+   * opt-in transcript sources, this reads nothing new, writes only suggestions
+   * (never `supersedes`), and stays affordable by construction: at most
+   * `maxPerSync` new SLM judgments per run, judged pairs memoized and never
+   * re-asked, and an unreachable model degrades to skipping quietly.
+   */
+  contradictions: z.object({
+    autoCheck: z.boolean().default(true),
+    maxPerSync: z.number().int().nonnegative().default(3),
+    /** Ollama model tag. Must be pulled locally, same as `sources.session.model`. */
+    model: z.string().default(DEFAULT_SLM_MODEL)
+  }).default({ autoCheck: true, maxPerSync: 3, model: DEFAULT_SLM_MODEL })
 });
 function defaultConfig(projectId) {
   return ConfigSchema.parse({ version: 1, projectId });
@@ -944,13 +957,32 @@ UPDATE nodes SET provenance = 'observed' WHERE kind IN ('git_commit', 'code_diff
 
 CREATE INDEX idx_nodes_supersedes ON nodes (supersedes) WHERE supersedes IS NOT NULL;
 `;
+var V7 = `
+UPDATE nodes SET provenance = 'authored' WHERE kind IN ('doc_section', 'note');
+UPDATE nodes SET provenance = 'recorded' WHERE kind = 'conversation_turn';
+UPDATE nodes SET provenance = 'derived'  WHERE kind = 'session_summary';
+UPDATE nodes SET provenance = 'recorded' WHERE provenance = 'inferred';
+`;
+var V8 = `
+CREATE TABLE contradiction_checks (
+  candidate_id TEXT NOT NULL REFERENCES nodes (id) ON DELETE CASCADE,
+  against_id   TEXT NOT NULL REFERENCES nodes (id) ON DELETE CASCADE,
+  contradicts  INTEGER NOT NULL,
+  reason       TEXT,
+  model        TEXT NOT NULL,
+  checked_at   INTEGER NOT NULL,
+  PRIMARY KEY (candidate_id, against_id)
+);
+`;
 var MIGRATIONS = [
   { version: 1, up: (db) => db.exec(V1) },
   { version: 2, up: (db) => db.exec(V2) },
   { version: 3, up: (db) => db.exec(V3) },
   { version: 4, up: (db) => db.exec(V4) },
   { version: 5, up: (db) => db.exec(V5) },
-  { version: 6, up: (db) => db.exec(V6) }
+  { version: 6, up: (db) => db.exec(V6) },
+  { version: 7, up: (db) => db.exec(V7) },
+  { version: 8, up: (db) => db.exec(V8) }
 ];
 var LATEST_SCHEMA_VERSION = MIGRATIONS[MIGRATIONS.length - 1]?.version ?? 0;
 function currentSchemaVersion(db) {
@@ -1012,11 +1044,13 @@ function defaultProvenanceForKind(kind) {
     case "code_diff":
     case "shell_command":
       return "observed";
-    case "conversation_turn":
-    case "session_summary":
     case "doc_section":
     case "note":
-      return "inferred";
+      return "authored";
+    case "conversation_turn":
+      return "recorded";
+    case "session_summary":
+      return "derived";
   }
 }
 
@@ -1171,7 +1205,7 @@ function listStaleCandidates(db, projectId, opts = {}) {
   const rows = db.prepare(
     `SELECT id, kind, ts, ts_epoch AS tsEpoch, source, title
        FROM nodes
-       WHERE project_id = @projectId AND provenance = 'inferred' AND ts_epoch < @cutoff
+       WHERE project_id = @projectId AND provenance != 'observed' AND ts_epoch < @cutoff
          AND id NOT IN (SELECT supersedes FROM nodes WHERE project_id = @projectId AND supersedes IS NOT NULL)
        ORDER BY ts_epoch ASC
        LIMIT @limit`
@@ -1191,7 +1225,7 @@ function countStaleCandidates(db, projectId, opts = {}) {
   const cutoff = now.getTime() - minAgeDays * 864e5;
   const row = db.prepare(
     `SELECT COUNT(*) AS count FROM nodes
-       WHERE project_id = @projectId AND provenance = 'inferred' AND ts_epoch < @cutoff
+       WHERE project_id = @projectId AND provenance != 'observed' AND ts_epoch < @cutoff
          AND id NOT IN (SELECT supersedes FROM nodes WHERE project_id = @projectId AND supersedes IS NOT NULL)`
   ).get({ projectId, cutoff });
   return row.count;
@@ -1372,6 +1406,11 @@ function countNodesNeedingEmbedding(db, projectId) {
   ).get(projectId);
   return row.n;
 }
+function getEmbedding(db, nodeId) {
+  const row = db.prepare("SELECT v.embedding AS embedding FROM nodes_vec v JOIN nodes n ON n.rowid = v.rowid WHERE n.id = ?").get(nodeId);
+  if (!row) return null;
+  return new Float32Array(row.embedding.buffer, row.embedding.byteOffset, row.embedding.byteLength / 4);
+}
 function upsertEmbedding(db, rowid, embedding) {
   db.prepare("INSERT OR REPLACE INTO nodes_vec (rowid, embedding) VALUES (?, ?)").run(BigInt(rowid), embedding);
 }
@@ -1449,6 +1488,49 @@ function setMeta(db, key, value) {
   );
 }
 
+// src/store/contradictions.ts
+function recordContradictionCheck(db, input) {
+  db.prepare(
+    `INSERT OR REPLACE INTO contradiction_checks (candidate_id, against_id, contradicts, reason, model, checked_at)
+     VALUES (@candidateId, @againstId, @contradicts, @reason, @model, @now)`
+  ).run({
+    candidateId: input.candidateId,
+    againstId: input.againstId,
+    contradicts: input.contradicts ? 1 : 0,
+    reason: input.reason,
+    model: input.model,
+    now: Date.now()
+  });
+}
+function hasContradictionCheck(db, candidateId, againstId) {
+  const row = db.prepare("SELECT 1 FROM contradiction_checks WHERE candidate_id = ? AND against_id = ?").get(candidateId, againstId);
+  return row !== void 0;
+}
+function listContradictionSuggestions(db, projectId, opts = {}) {
+  return db.prepare(
+    `SELECT c.candidate_id AS candidateId, n.title AS candidateTitle,
+              c.against_id AS againstId, a.title AS againstTitle,
+              c.reason AS reason, c.checked_at AS checkedAt
+       FROM contradiction_checks c
+       JOIN nodes n ON n.id = c.candidate_id
+       JOIN nodes a ON a.id = c.against_id
+       WHERE n.project_id = @projectId AND c.contradicts = 1
+         AND c.candidate_id NOT IN (SELECT supersedes FROM nodes WHERE project_id = @projectId AND supersedes IS NOT NULL)
+       ORDER BY c.checked_at DESC
+       LIMIT @limit`
+  ).all({ projectId, limit: opts.limit ?? 50 });
+}
+function countContradictionSuggestions(db, projectId) {
+  const row = db.prepare(
+    `SELECT COUNT(*) AS count
+       FROM contradiction_checks c
+       JOIN nodes n ON n.id = c.candidate_id
+       WHERE n.project_id = @projectId AND c.contradicts = 1
+         AND c.candidate_id NOT IN (SELECT supersedes FROM nodes WHERE project_id = @projectId AND supersedes IS NOT NULL)`
+  ).get({ projectId });
+  return row.count;
+}
+
 // src/store/store.ts
 var MemoryStore = class _MemoryStore {
   constructor(db) {
@@ -1608,6 +1690,10 @@ var MemoryStore = class _MemoryStore {
   upsertEmbedding(rowid, embedding) {
     upsertEmbedding(this.db, rowid, embedding);
   }
+  /** The stored vector for one node, or null if it has not been embedded yet. */
+  getEmbedding(nodeId) {
+    return getEmbedding(this.db, nodeId);
+  }
   dropAllEmbeddings() {
     return dropAllEmbeddings(this.db);
   }
@@ -1638,7 +1724,7 @@ var MemoryStore = class _MemoryStore {
   setSupersedes(newNodeId, staleNodeId) {
     setSupersedes(this.db, newNodeId, staleNodeId);
   }
-  /** Aging `inferred` nodes nothing supersedes yet -- candidates for `nexusmem mark-stale`, not auto-applied. */
+  /** Aging non-`observed` nodes nothing supersedes yet -- candidates for `nexusmem mark-stale`, not auto-applied. */
   listStaleCandidates(projectId, opts = {}) {
     return listStaleCandidates(this.db, projectId, opts);
   }
@@ -1646,6 +1732,20 @@ var MemoryStore = class _MemoryStore {
   countStaleCandidates(projectId, opts = {}) {
     return countStaleCandidates(this.db, projectId, opts);
   }
+  /** Memoize one SLM contradiction judgment (either verdict). Suggest-only: never writes `supersedes`. */
+  recordContradictionCheck(input) {
+    recordContradictionCheck(this.db, input);
+  }
+  hasContradictionCheck(candidateId, againstId) {
+    return hasContradictionCheck(this.db, candidateId, againstId);
+  }
+  /** Open YES verdicts awaiting a human's `mark-stale`, newest judgment first. */
+  listContradictionSuggestions(projectId, opts = {}) {
+    return listContradictionSuggestions(this.db, projectId, opts);
+  }
+  countContradictionSuggestions(projectId) {
+    return countContradictionSuggestions(this.db, projectId);
+  }
   /** Escape hatch for tests and future modules. */
   get raw() {
     return this.db;
@@ -2458,7 +2558,12 @@ var SIGNAL_FLOOR = 0.2;
 var RECENCY_FLOOR = 0.3;
 var DEFAULT_HALF_LIFE_DAYS = 30;
 var MS_PER_DAY = 864e5;
-var INFERRED_HALF_LIFE_RATIO = 0.5;
+var HALF_LIFE_RATIO = {
+  observed: 1,
+  authored: 0.75,
+  recorded: 0.5,
+  derived: 0.35
+};
 var SUPERSEDED_PENALTY = 0.5;
 var MAX_PRIOR_OVERTURN = 2;
 var PRIOR_COUNT = 2;
@@ -2493,14 +2598,14 @@ function ageDaysOf(ts, now) {
 function rankHits(hits, opts = {}) {
   if (hits.length === 0) return [];
   const halfLife = opts.halfLifeDays ?? DEFAULT_HALF_LIFE_DAYS;
-  const inferredHalfLife = opts.inferredHalfLifeDays ?? halfLife * INFERRED_HALF_LIFE_RATIO;
+  const ratios = { ...HALF_LIFE_RATIO, ...opts.halfLifeRatios };
   const now = opts.now ?? /* @__PURE__ */ new Date();
   const relevances = opts.relevanceScores ? normalizeExternalRelevance(hits, opts.relevanceScores) : normalizeRelevance(hits);
   const ranked = hits.map((hit, i) => {
     const relevance = relevances[i] ?? RELEVANCE_FLOOR;
     const signalWeight = SIGNAL_FLOOR + (1 - SIGNAL_FLOOR) * hit.signal;
     const ageDays = ageDaysOf(hit.ts, now);
-    const effectiveHalfLife = hit.provenance === "inferred" ? inferredHalfLife : halfLife;
+    const effectiveHalfLife = halfLife * (ratios[hit.provenance] ?? 1);
     const recencyFactor = RECENCY_FLOOR + (1 - RECENCY_FLOOR) * 2 ** (-ageDays / effectiveHalfLife);
     const rawScore = relevance * signalWeight ** SIGNAL_EXPONENT * recencyFactor ** RECENCY_EXPONENT;
     const score = opts.supersededIds?.has(hit.id) ? rawScore * SUPERSEDED_PENALTY : rawScore;
@@ -2830,8 +2935,8 @@ function toMemoryNodes(turn, projectId, opts = {}) {
       files: extractMentionedFiles(`${userRedacted.text}
 ${chunk2.text}`),
       signal: scoreConversationTurn(userRedacted.text, chunk2.text),
-      provenance: "inferred",
-      // discourse about what happened, not the event itself
+      provenance: "recorded",
+      // verbatim discourse about what happened, not the event itself
       meta: {
         cwd: turn.cwd,
         source: turn.source,
@@ -3403,8 +3508,8 @@ function toMemoryNodes3(file, projectId, opts = {}) {
       body: truncate(chunk2.text, maxBody),
       files: [{ path: file.path, insertions: null, deletions: null, binary: false }],
       signal: scoreDocSection(file.path, chunk2.heading, chunk2.text),
-      provenance: "inferred",
-      // a written claim, and the kind of content most likely to go stale
+      provenance: "authored",
+      // a human's own written claim -- deliberate, but can still go stale
       meta: {
         path: file.path,
         heading: chunk2.heading,
@@ -3566,7 +3671,7 @@ ${summary.body}`;
     files: extractMentionedFiles(session.turns.map((t) => `${t.userText}
 ${t.assistantText}`).join("\n")),
     signal: scoreSession(session.turns.length),
-    provenance: "inferred",
+    provenance: "derived",
     // a model's distillation, not a directly observed event
     meta: {
       sessionKey: session.sessionKey,
@@ -3820,6 +3925,97 @@ async function readDocFiles(repoRoot, opts = {}) {
   return { files, unreadable };
 }
 
+// src/slm/contradiction.ts
+var MAX_BODY_CHARS = 1500;
+var MAX_REASON_CHARS = 200;
+var CONTRADICTION_INSTRUCTIONS = `You are checking whether a NEWER memory replaces or contradicts an OLDER one, for an AI coding assistant's memory index.
+
+Answer in exactly this shape:
+VERDICT: YES or NO
+REASON: <one line, under 20 words>
+
+Say YES only if the NEWER memory states something that makes the OLDER one factually wrong or obsolete -- a decision reversed, a bug fixed, a plan abandoned. Say NO if they are about different things, or the newer one only adds detail without contradicting the older one. When unsure, say NO.`;
+function buildContradictionPrompt(older, newer) {
+  const body = [
+    `OLDER (${older.title}):`,
+    truncate(older.body, MAX_BODY_CHARS),
+    "",
+    `NEWER (${newer.title}):`,
+    truncate(newer.body, MAX_BODY_CHARS)
+  ].join("\n");
+  return `${CONTRADICTION_INSTRUCTIONS}
+
+---
+
+${body}
+
+---
+
+Answer:`;
+}
+function parseContradictionVerdict(raw) {
+  const lines = raw.trim().split(/\r?\n/).map((l) => l.trim()).filter((l) => l.length > 0);
+  const verdictLine = lines.find((l) => /^VERDICT:/i.test(l));
+  if (!verdictLine) return null;
+  const verdict = /^VERDICT:\s*(YES|NO)\b/i.exec(verdictLine);
+  if (!verdict) return null;
+  const reasonLine = lines.find((l) => /^REASON:/i.test(l));
+  const reason = reasonLine ? reasonLine.replace(/^REASON:\s*/i, "").trim() : "";
+  return {
+    contradicts: verdict[1].toUpperCase() === "YES",
+    reason: truncate(reason, MAX_REASON_CHARS)
+  };
+}
+
+// src/retrieval/contradiction.ts
+var DEFAULT_LIMIT = 10;
+var DEFAULT_NEIGHBOR_LIMIT = 25;
+async function checkContradictions(store, embeddingProvider, slmProvider, projectId, candidates, opts = {}) {
+  const limit = opts.limit ?? DEFAULT_LIMIT;
+  const neighborLimit = opts.neighborLimit ?? DEFAULT_NEIGHBOR_LIMIT;
+  const model = opts.model ?? DEFAULT_SLM_MODEL;
+  const suggestions = [];
+  let judgments = 0;
+  let consecutiveNullReplies = 0;
+  for (const candidate of candidates.slice(0, limit)) {
+    if (opts.maxJudgments !== void 0 && judgments >= opts.maxJudgments) break;
+    const full = store.getNodesByIds([candidate.id])[0];
+    if (!full) continue;
+    const embedding = store.getEmbedding(candidate.id) ?? await embeddingProvider.embed(`${full.title}
+${full.body}`);
+    if (!embedding) continue;
+    const candidateEpoch = Date.parse(candidate.ts);
+    const nearest = store.vectorSearch(projectId, embedding, neighborLimit + 1).find((hit) => hit.id !== candidate.id && Date.parse(hit.ts) > candidateEpoch);
+    if (!nearest) continue;
+    if (store.hasContradictionCheck(candidate.id, nearest.id)) continue;
+    const reply = await slmProvider.complete(buildContradictionPrompt(full, nearest));
+    if (!reply) {
+      consecutiveNullReplies += 1;
+      if (consecutiveNullReplies >= 2) break;
+      continue;
+    }
+    consecutiveNullReplies = 0;
+    const verdict = parseContradictionVerdict(reply);
+    if (!verdict) continue;
+    judgments += 1;
+    store.recordContradictionCheck({
+      candidateId: candidate.id,
+      againstId: nearest.id,
+      contradicts: verdict.contradicts,
+      reason: verdict.contradicts ? verdict.reason : null,
+      model
+    });
+    if (!verdict.contradicts) continue;
+    suggestions.push({
+      candidateId: candidate.id,
+      againstId: nearest.id,
+      againstTitle: nearest.title,
+      reason: verdict.reason
+    });
+  }
+  return suggestions;
+}
+
 // src/shell/detect.ts
 import { existsSync as existsSync4 } from "fs";
 import { readFile as readFile9, stat as stat2 } from "fs/promises";
@@ -4216,6 +4412,8 @@ function extractPhpIncludeSpecifiers(source) {
 
 // src/structure/extract-python.ts
 var RELATIVE_IMPORT_PATTERN = /\bfrom\s+(\.+)([\w.]*)\s+import\s+([^\n]+)/g;
+var BARE_FROM_IMPORT_PATTERN = /^[ \t]*from\s+([A-Za-z_]\w*)\s+import\b/gm;
+var BARE_IMPORT_PATTERN = /^[ \t]*import\s+([^\n]+)/gm;
 function cleanNames(raw) {
   return raw.split("#")[0].replace(/[()]/g, "").split(",").map((token) => token.trim().split(/\s+as\s+/)[0].trim()).filter((name) => /^[A-Za-z_]\w*$/.test(name));
 }
@@ -4234,6 +4432,16 @@ function extractPythonImportSpecifiers(source) {
       seen.add(dots + name);
     }
   }
+  BARE_FROM_IMPORT_PATTERN.lastIndex = 0;
+  while ((match = BARE_FROM_IMPORT_PATTERN.exec(source)) !== null) {
+    seen.add(match[1]);
+  }
+  BARE_IMPORT_PATTERN.lastIndex = 0;
+  while ((match = BARE_IMPORT_PATTERN.exec(source)) !== null) {
+    for (const name of cleanNames(match[1])) {
+      seen.add(name);
+    }
+  }
   return [...seen];
 }
 
@@ -4314,7 +4522,9 @@ function resolveJavaSpecifier(specifier, trackedPaths) {
   if (segments.length === 0) return [];
   if (isWildcard) {
     const dirSuffix = segments.join("/");
-    return [...trackedPaths].filter((p) => p.endsWith(".java") && endsAtSegmentBoundary(posix3.dirname(p), dirSuffix)).sort();
+    const matches2 = [...trackedPaths].filter((p) => p.endsWith(".java") && endsAtSegmentBoundary(posix3.dirname(p), dirSuffix));
+    const dirs = new Set(matches2.map((p) => posix3.dirname(p)));
+    return dirs.size === 1 ? matches2.sort() : [];
   }
   const fileSuffix = `${segments.join("/")}.java`;
   const matches = [...trackedPaths].filter((p) => endsAtSegmentBoundary(p, fileSuffix));
@@ -4335,11 +4545,182 @@ function resolvePhpSpecifier(fromPath, specifier, trackedPaths) {
 
 // src/structure/resolve-python.ts
 import { posix as posix5 } from "path";
+var STDLIB_MODULES = /* @__PURE__ */ new Set([
+  "__future__",
+  "abc",
+  "argparse",
+  "array",
+  "ast",
+  "asyncio",
+  "base64",
+  "bisect",
+  "builtins",
+  "calendar",
+  "cgi",
+  "cgitb",
+  "cmd",
+  "codecs",
+  "collections",
+  "colorsys",
+  "compileall",
+  "concurrent",
+  "configparser",
+  "contextlib",
+  "contextvars",
+  "copy",
+  "copyreg",
+  "cProfile",
+  "csv",
+  "ctypes",
+  "curses",
+  "dataclasses",
+  "datetime",
+  "dbm",
+  "decimal",
+  "difflib",
+  "dis",
+  "doctest",
+  "email",
+  "encodings",
+  "ensurepip",
+  "enum",
+  "errno",
+  "faulthandler",
+  "fcntl",
+  "filecmp",
+  "fileinput",
+  "fnmatch",
+  "fractions",
+  "ftplib",
+  "functools",
+  "gc",
+  "getopt",
+  "getpass",
+  "gettext",
+  "glob",
+  "graphlib",
+  "grp",
+  "gzip",
+  "hashlib",
+  "heapq",
+  "hmac",
+  "html",
+  "http",
+  "imaplib",
+  "importlib",
+  "inspect",
+  "io",
+  "ipaddress",
+  "itertools",
+  "json",
+  "keyword",
+  "locale",
+  "logging",
+  "lzma",
+  "mailbox",
+  "marshal",
+  "math",
+  "mimetypes",
+  "mmap",
+  "msvcrt",
+  "multiprocessing",
+  "operator",
+  "os",
+  "pathlib",
+  "pdb",
+  "pickle",
+  "pickletools",
+  "pkgutil",
+  "platform",
+  "plistlib",
+  "poplib",
+  "posix",
+  "pprint",
+  "profile",
+  "pstats",
+  "pty",
+  "pwd",
+  "py_compile",
+  "pyclbr",
+  "pydoc",
+  "queue",
+  "quopri",
+  "random",
+  "re",
+  "readline",
+  "reprlib",
+  "resource",
+  "rlcompleter",
+  "runpy",
+  "sched",
+  "secrets",
+  "select",
+  "selectors",
+  "shelve",
+  "shlex",
+  "shutil",
+  "signal",
+  "site",
+  "smtplib",
+  "socket",
+  "socketserver",
+  "sqlite3",
+  "ssl",
+  "stat",
+  "statistics",
+  "string",
+  "stringprep",
+  "struct",
+  "subprocess",
+  "symtable",
+  "sys",
+  "sysconfig",
+  "syslog",
+  "tarfile",
+  "telnetlib",
+  "tempfile",
+  "termios",
+  "test",
+  "textwrap",
+  "threading",
+  "time",
+  "timeit",
+  "tkinter",
+  "token",
+  "tokenize",
+  "tomllib",
+  "trace",
+  "traceback",
+  "tracemalloc",
+  "tty",
+  "turtle",
+  "types",
+  "typing",
+  "unicodedata",
+  "unittest",
+  "urllib",
+  "uuid",
+  "venv",
+  "warnings",
+  "wave",
+  "weakref",
+  "webbrowser",
+  "winreg",
+  "winsound",
+  "wsgiref",
+  "xml",
+  "xmlrpc",
+  "zipapp",
+  "zipfile",
+  "zipimport",
+  "zlib",
+  "zoneinfo"
+]);
 function resolvePythonSpecifier(fromPath, specifier, trackedPaths) {
   const dotsMatch = specifier.match(/^\.+/);
-  if (!dotsMatch) return null;
-  const level = dotsMatch[0].length;
-  const segments = specifier.slice(level).split(".").filter(Boolean);
+  const level = dotsMatch ? dotsMatch[0].length : 0;
+  if (level === 0 && STDLIB_MODULES.has(specifier)) return null;
+  const segments = (level === 0 ? specifier : specifier.slice(level)).split(".").filter(Boolean);
   if (segments.length === 0) return null;
   let dir = posix5.dirname(fromPath);
   for (let i = 1; i < level; i++) {
@@ -4744,6 +5125,21 @@ function runPruneSources(store, projectId, otherProjectIds, sources, yes, out) {
 `);
   return 0;
 }
+async function runAutoContradictionCheck(store, config, projectId, providers) {
+  if (!config.contradictions.autoCheck) return "";
+  const candidates = store.listStaleCandidates(projectId);
+  if (candidates.length === 0) return "";
+  const fresh = await checkContradictions(store, providers.embedder, providers.slm, projectId, candidates, {
+    limit: candidates.length,
+    maxJudgments: config.contradictions.maxPerSync,
+    model: config.contradictions.model
+  });
+  const open = store.countContradictionSuggestions(projectId);
+  if (fresh.length === 0 && open === 0) return "";
+  const freshPart = fresh.length > 0 ? pc7.yellow(`${fresh.length} new`) : `${fresh.length} new`;
+  return `  ${pc7.dim("contradictions:")} ${freshPart}${pc7.dim(`, ${open} open suggestion(s) -- run`)} ${pc7.bold("nexusmem stale")} ${pc7.dim("for detail")}
+`;
+}
 async function runSync(opts) {
   const { repo, ws, projectId, config } = await loadContext(opts.cwd);
   const log = (line) => {
@@ -4797,6 +5193,7 @@ async function runSync(opts) {
     const docs = await syncDocs(store, projectId, repo.root, config, log);
     const structure = await syncStructure(store, projectId, repo.root, config, log);
     let embedLine = "";
+    let embeddingAvailable = false;
     if (!opts.noEmbed) {
       let lastLogged = 0;
       const result = await embedPendingNodes(store, new OllamaEmbeddingProvider(), projectId, {
@@ -4808,6 +5205,7 @@ async function runSync(opts) {
           log(`  ${pc7.dim(`vector: ${attempted}/${total} embedded`)}`);
         }
       });
+      embeddingAvailable = !result.providerUnavailable;
       if (result.embedded > 0) {
         const skippedPart = result.skipped > 0 ? pc7.dim(`, ${result.skipped} skipped`) : "";
         const remainingPart = result.remaining > 0 ? pc7.yellow(`, ${result.remaining} still pending`) : "";
@@ -4817,6 +5215,10 @@ async function runSync(opts) {
         log(`${pc7.dim("vector")} embedding provider unavailable (is Ollama running with nomic-embed-text pulled?) -- BM25-only for now`);
       }
     }
+    const contradictionLine = !opts.noEmbed && embeddingAvailable ? await runAutoContradictionCheck(store, config, projectId, {
+      embedder: new OllamaEmbeddingProvider(),
+      slm: new OllamaChatProvider({ model: config.contradictions.model })
+    }) : "";
     let linkLine = "";
     if (opts.linkFailures) {
       const linkStats = correlateFailures(store, projectId);
@@ -4845,7 +5247,7 @@ async function runSync(opts) {
         `  ${pc7.green(`+${totals.inserted} new`)}  ${pc7.yellow(`~${totals.updated} updated`)}  ${pc7.dim(`=${totals.unchanged} unchanged`)}${deniedPart}`,
         `  ${pc7.dim(`${stats2.total} node(s) total across ${stats2.distinctFiles} file path(s)`)}`,
         ""
-      ].join("\n") + embedLine + linkLine
+      ].join("\n") + embedLine + linkLine + contradictionLine
     );
     return 0;
   } finally {
@@ -5602,6 +6004,7 @@ ${pc17.bold(String(edges.length))} edge(s) from ${filesScanned} tracked ${TRACKE
 
 // src/cli/commands/stale.ts
 import pc18 from "picocolors";
+var STALE_DEFAULT_MODEL = DEFAULT_SLM_MODEL;
 async function runStale(opts) {
   const { projectId, ws } = await loadContext(opts.cwd);
   const out = opts.out ?? ((chunk2) => void process.stdout.write(chunk2));
@@ -5609,16 +6012,35 @@ async function runStale(opts) {
   try {
     const candidates = store.listStaleCandidates(projectId, { minAgeDays: opts.minAgeDays, limit: opts.limit });
     if (candidates.length === 0) {
-      out(`${pc18.dim("no stale candidates")} -- no inferred node older than the threshold lacks a successor
+      out(`${pc18.dim("no stale candidates")} -- no unconfirmed node older than the threshold lacks a successor
 `);
       return 0;
     }
+    let suggestions = [];
+    if (opts.checkContradictions) {
+      suggestions = await checkContradictions(
+        store,
+        new OllamaEmbeddingProvider(),
+        new OllamaChatProvider({ model: opts.model ?? DEFAULT_SLM_MODEL }),
+        projectId,
+        candidates,
+        { model: opts.model ?? DEFAULT_SLM_MODEL }
+      );
+    }
+    const byCandidateId = /* @__PURE__ */ new Map();
+    for (const s of store.listContradictionSuggestions(projectId)) {
+      byCandidateId.set(s.candidateId, { againstId: s.againstId, againstTitle: s.againstTitle, reason: s.reason ?? "" });
+    }
+    for (const s of suggestions) byCandidateId.set(s.candidateId, s);
     out(
       [
         `${pc18.bold(String(candidates.length))} stale candidate(s) -- oldest first, none of these were changed:`,
-        ...candidates.map(
-          (c) => `  ${pc18.dim(c.id)} ${pc18.yellow(`${c.ageDays}d old`)} [${c.kind}] ${c.title}`
-        ),
+        ...candidates.map((c) => {
+          const line = `  ${pc18.dim(c.id)} ${pc18.yellow(`${c.ageDays}d old`)} [${c.kind}] ${c.title}`;
+          const hit = byCandidateId.get(c.id);
+          return hit ? `${line}
+    ${pc18.red("likely superseded by")} ${pc18.dim(hit.againstId)} ${hit.againstTitle} -- ${hit.reason}` : line;
+        }),
         "",
         `run ${pc18.bold("nexusmem mark-stale <id> --supersedes <newId>")} on any that are actually wrong`
       ].join("\n").concat("\n")
@@ -5689,6 +6111,7 @@ async function runStatus(opts) {
     const otherProjectNodes = store.countProjectNodes(otherProjectIds);
     const structure = store.fileEdgeStats(projectId);
     const staleCount = store.countStaleCandidates(projectId);
+    const flaggedCount = store.countContradictionSuggestions(projectId);
     const dbBytes = fileSize(ws.dbPath) + fileSize(`${ws.dbPath}-wal`);
     const kinds = Object.entries(stats2.byKind).sort((a, b) => b[1] - a[1]).map(([kind, n]) => `    ${String(n).padStart(6)}  ${kind}`);
     const staleProjectWarning = otherProjectIds.length ? `${pc19.yellow("stale   ")} ${otherProjectIds.length} prior project ${otherProjectIds.length === 1 ? "identity holds" : "identities hold"} ${otherProjectNodes} node(s) \u2014 run ${pc19.bold(
@@ -5717,7 +6140,8 @@ async function runStatus(opts) {
         gitCursor && gitCursor !== repo.head ? `${pc19.yellow("git behind HEAD")} \u2014 run ${pc19.bold("nexusmem sync")}` : "",
         chains.failuresTotal ? `${pc19.dim("chains  ")} ${pc19.bold(String(chains.resolvedTotal))}/${chains.failuresTotal} failure(s) resolved ${pc19.dim(`(${chains.resolvedByRetry} retry, ${chains.resolvedByDiscussion} discussion)`)}${chains.resolvedTotal < chains.failuresTotal ? ` \u2014 run ${pc19.bold("nexusmem sync --link-failures")} to link more` : ""}` : "",
         structure.edges ? `${pc19.dim("structure")} ${pc19.bold(String(structure.edges))} import edge(s) across ${structure.files} file(s)` : "",
-        staleCount ? `${pc19.dim("aging   ")} ${pc19.bold(String(staleCount))} inferred node(s) worth a look \u2014 run ${pc19.bold("nexusmem stale")}` : ""
+        staleCount ? `${pc19.dim("aging   ")} ${pc19.bold(String(staleCount))} unconfirmed node(s) worth a look \u2014 run ${pc19.bold("nexusmem stale")}` : "",
+        flaggedCount ? `${pc19.dim("flagged ")} ${pc19.bold(String(flaggedCount))} likely-superseded node(s) awaiting review \u2014 run ${pc19.bold("nexusmem stale")} for detail` : ""
       ].filter((line) => line !== "").join("\n").concat("\n")
     );
     return 0;
@@ -5839,8 +6263,19 @@ program.command("mark-stale").description(
 ).argument("<nodeId>", "id of the node to mark stale").requiredOption("--supersedes <newNodeId>", "id of the node that supersedes it").option("-C, --cwd <path>", "repository path", process.cwd()).action(
   (nodeId, options) => guard(() => runMarkStale({ cwd: options.cwd, nodeId, supersedesId: options.supersedes }))()
 );
-program.command("stale").description("List inferred nodes old enough to be worth double-checking (writes nothing)").option("-C, --cwd <path>", "repository path", process.cwd()).option("--min-age-days <days>", "only nodes at least this old", (v) => Number.parseFloat(v)).option("-n, --limit <count>", "stop after N candidates", (v) => Number.parseInt(v, 10)).action(
-  (options) => guard(() => runStale({ cwd: options.cwd, minAgeDays: options.minAgeDays, limit: options.limit }))()
+program.command("stale").description("List unconfirmed (non-observed) nodes old enough to be worth double-checking (writes nothing)").option("-C, --cwd <path>", "repository path", process.cwd()).option("--min-age-days <days>", "only nodes at least this old", (v) => Number.parseFloat(v)).option("-n, --limit <count>", "stop after N candidates", (v) => Number.parseInt(v, 10)).option(
+  "--check-contradictions",
+  "ask the local SLM whether a similar newer node actually contradicts each candidate (needs Ollama)"
+).option("--model <name>", "Ollama chat model for --check-contradictions", STALE_DEFAULT_MODEL).action(
+  (options) => guard(
+    () => runStale({
+      cwd: options.cwd,
+      minAgeDays: options.minAgeDays,
+      limit: options.limit,
+      checkContradictions: options.checkContradictions,
+      model: options.model
+    })
+  )()
 );
 program.command("projects").description("List the repositories `query --all-projects` would search").option("--prune", "forget registered projects whose database is no longer on disk", false).option("--json", "emit the registry as JSON on stdout", false).action((options) => guard(() => runProjects({ prune: options.prune, json: options.json }))());
 program.command("scan-git").description("Preview the MemoryNodes git history would produce (writes nothing)").option("-C, --cwd <path>", "repository path", process.cwd()).option("--since <date>", "only commits newer than this git date expression, e.g. 90.days.ago").option("-n, --limit <count>", "stop after N commits", (v) => Number.parseInt(v, 10)).option("--no-merges", "skip merge commits").option("--min-signal <score>", "drop nodes below this signal", (v) => Number.parseFloat(v), 0).option("--json", "emit MemoryNodes as JSON on stdout", false).action(
@@ -5898,7 +6333,7 @@ program.command("precheck").description("Warn about staged files with unresolved
     })
   )()
 );
-program.command("scan-structure").description("Preview the JS/TS/Python import-graph edges a sync would produce (writes nothing)").option("-C, --cwd <path>", "repository path", process.cwd()).option("--json", "emit edges as JSON on stdout", false).action((options) => guard(() => runScanStructure({ cwd: options.cwd, json: options.json }))());
+program.command("scan-structure").description("Preview the JS/TS/Python/Go/Rust/Java/PHP import-graph edges a sync would produce (writes nothing)").option("-C, --cwd <path>", "repository path", process.cwd()).option("--json", "emit edges as JSON on stdout", false).action((options) => guard(() => runScanStructure({ cwd: options.cwd, json: options.json }))());
 program.command("mcp").description("Start the MCP server (stdio transport) for Claude Desktop, Cursor, Windsurf, etc.").action(() => guard(() => runMcpServer().then(() => 0))());
 program.parseAsync(process.argv).catch((err) => {
   const message = err instanceof Error ? err.message : String(err);