@theglitchking/semantic-memory 1.2.2 → 1.5.1

package/dist/cli/index.js

@@ -7,6 +7,46 @@ import { resolve as resolve2, join as join3, dirname, relative } from "path";
 import { existsSync as existsSync3, readFileSync, writeFileSync, rmSync } from "fs";
 import { createRequire } from "module";
 import { spawnSync } from "child_process";
+import { pathToFileURL } from "url";
+
+// src/core/healthcheck-fix.ts
+var MANUAL_REASON = {
+  "regenerate-contract": "AGENTS.md needs a human decision \u2014 run `/contract` (regenerate_contract), or move custom content into a Local Notes section outside the managed block.",
+  lint_vault: "Vault lint findings (stale notes, broken wikilinks, schema violations) require human review \u2014 run `lint_vault` for the full report.",
+  session_staleness: "Resume the session (session_run / session_finish) or remove .claude/.semantic-memory/session.json to abandon it."
+};
+function planFixes(findings) {
+  const fixes = [];
+  const skipped = [];
+  for (const f of findings) {
+    if (f.severity === "ok") continue;
+    switch (f.fixable_via) {
+      case "skill-link":
+        fixes.push({ check: f.check, action: "skill-link", summary: f.summary });
+        break;
+      case "mcp-reconcile":
+        fixes.push({ check: f.check, action: "mcp-reconcile", summary: f.summary });
+        break;
+      case "reindex":
+        fixes.push({ check: f.check, action: "reindex", summary: f.summary });
+        break;
+      case "state-migrate":
+        fixes.push({ check: f.check, action: "state-migrate", summary: f.summary });
+        break;
+      case "regenerate-contract":
+        skipped.push({ check: f.check, reason: MANUAL_REASON["regenerate-contract"] });
+        break;
+      default:
+        skipped.push({
+          check: f.check,
+          reason: MANUAL_REASON[f.check] ?? "No automatic fix available \u2014 needs human review."
+        });
+    }
+  }
+  return { fixes, skipped };
+}
+
+// src/cli/index.ts
 import { registerUpdateCommands } from "@theglitchking/claude-plugin-runtime";
 
 // src/cli/skills.ts
@@ -287,6 +327,61 @@ function runRelink(cwd) {
     stdio: "inherit"
   });
 }
+async function executeFixes(cwd, fixes) {
+  const outcomes = [];
+  const actions = [...new Set(fixes.map((f) => f.action))];
+  for (const action of actions) {
+    const checks = fixes.filter((f) => f.action === action).map((f) => f.check).join(", ");
+    try {
+      switch (action) {
+        case "skill-link": {
+          runRelink(cwd);
+          outcomes.push({ check: checks, action, status: "fixed", detail: "re-linked skills" });
+          break;
+        }
+        case "state-migrate": {
+          const r = migrateState({ projectRoot: cwd, force: true });
+          outcomes.push({
+            check: checks,
+            action,
+            status: "fixed",
+            detail: `migrated ${r.migrated.length} file(s), resolved ${r.conflicts.length} conflict(s)`
+          });
+          break;
+        }
+        case "mcp-reconcile": {
+          const reconcilePath = join3(findSourceRoot(), "hooks", "reconcile.js");
+          if (!existsSync3(reconcilePath)) {
+            outcomes.push({ check: checks, action, status: "failed", detail: "reconcile.js not found" });
+            break;
+          }
+          const mod = await import(pathToFileURL(reconcilePath).href);
+          mod.reconcile(cwd);
+          outcomes.push({ check: checks, action, status: "fixed", detail: "reconciled .mcp.json" });
+          break;
+        }
+        case "reindex": {
+          const bin = findLocalBin(cwd);
+          if (!bin) {
+            outcomes.push({ check: checks, action, status: "failed", detail: "no local bin to run reindex" });
+            break;
+          }
+          const vault = join3(cwd, ".claude", ".vault");
+          const r = spawnSync("node", [bin, "--notes", vault, "--reindex"], { cwd, stdio: "pipe", timeout: 12e4 });
+          if (r.status === 0) {
+            outcomes.push({ check: checks, action, status: "fixed", detail: "reindexed vault" });
+          } else {
+            outcomes.push({ check: checks, action, status: "failed", detail: (r.stderr?.toString() || "reindex failed").slice(0, 200) });
+          }
+          break;
+        }
+      }
+    } catch (err) {
+      outcomes.push({ check: checks, action, status: "failed", detail: err?.message ?? String(err) });
+    }
+  }
+  return outcomes;
+}
 function findLocalBin(cwd) {
   const candidates = [
     join3(cwd, "node_modules", "@theglitchking", "semantic-memory", "bin", "semantic-memory"),
@@ -526,7 +621,7 @@ program.name("semantic-memory").description(
   "Unified memory-layer MCP server for Claude Code (rebrand of semantic-sidekick at v1.0.0).\nThe `semantic-sidekick` command is preserved as an alias.\n\n  Start MCP server:  semantic-memory --notes ./vault\n  Show vault stats:  semantic-memory --notes ./vault --stats\n  Force reindex:     semantic-memory --notes ./vault --reindex\n  List MCP tools:    semantic-memory tools\n  Tool details:      semantic-memory tools search_semantic"
 ).version(version);
 program.command("search <query>").description("Run a vault search and print top hits as JSON (used by activation hooks)").requiredOption("--notes <path>", "Path to markdown notes directory").option("--limit <n>", "Max results", (v) => parseInt(v, 10), 8).option("--text-only", "Skip embedder \u2014 keyword-only search (fast path, no model init)").option("--json", "Emit raw JSON (default)", true).action(async (query, opts) => {
-  const { runSearch } = await import("../search-27WYAI24.js");
+  const { runSearch } = await import("../search-AHKEFI2B.js");
   try {
     const hits = await runSearch({
       notes: opts.notes,
@@ -542,7 +637,7 @@ program.command("search <query>").description("Run a vault search and print top
   }
 });
 program.command("lint").description("Lint the vault against vault.schema.yml (schema violations + missing provenance + stale)").requiredOption("--notes <path>", "Path to markdown notes directory").option("--rule <name>", "Limit output to one rule: schema_violations | missing_provenance | stale").option("--json", "Emit JSON instead of the human-readable report").option("--strict", "Exit non-zero on warnings too (default: exit non-zero only on errors)").action(async (opts) => {
-  const { lintVault, formatLintReport } = await import("../lint-GMXQF4RW.js");
+  const { lintVault, formatLintReport } = await import("../lint-XUQ7JDYX.js");
   const report = await lintVault(resolve2(opts.notes));
   if (opts.json) {
     const out = opts.rule ? report.byRule[opts.rule] : report;
@@ -593,7 +688,7 @@ program.command("log-query").description("Read structured log entries from log.m
   }
 });
 program.command("install-schema").description("Bootstrap vault.schema.yml in the vault root with the default schema").requiredOption("--notes <path>", "Path to markdown notes directory").option("--force", "Overwrite existing schema file").action(async (opts) => {
-  const { installDefaultSchema } = await import("../schema-F3RTY6SQ.js");
+  const { installDefaultSchema } = await import("../schema-ATFCLC6Y.js");
   const r = await installDefaultSchema(resolve2(opts.notes), opts.force);
   console.log(r.written ? `Installed default schema: ${r.path}` : `Schema already exists: ${r.path} (use --force to overwrite)`);
   process.exit(0);
@@ -613,7 +708,7 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
     process.exit(1);
   }
   if (opts.stats) {
-    const { Indexer } = await import("../indexer-KD6UTXZB.js");
+    const { Indexer } = await import("../indexer-YW4O3VVM.js");
     const indexer = new Indexer(notesPath);
     const docs = await indexer.indexAll();
     console.log(`Notes: ${docs.length}`);
@@ -722,8 +817,8 @@ ${verify.stderr?.toString() || ""}`);
   process.exit(0);
 });
 program.command("healthcheck").description(
-  "Verify the local install starts cleanly + run drift detection. Self-heals common npx-cache corruption (ERR_MODULE_NOT_FOUND). With --fast, skips the slow tier (full vault lint)."
-).option("--fast", "Run only the fast-tier drift checks (file-system probes). Skips the slow tier (full vault lint).", false).option("--json", "Emit structured JSON output instead of human-readable text.", false).action(async (opts) => {
+  "Verify the local install starts cleanly + run drift detection. Self-heals common npx-cache corruption (ERR_MODULE_NOT_FOUND). With --fast, skips the slow tier (full vault lint). With --fix, auto-applies safe fixes for fixable findings."
+).option("--fast", "Run only the fast-tier drift checks (file-system probes). Skips the slow tier (full vault lint).", false).option("--json", "Emit structured JSON output instead of human-readable text.", false).option("--fix", "Auto-apply safe fixes for fixable drift findings (re-link skills, reconcile .mcp.json, reindex, migrate state). Findings that need human review are reported, not touched.", false).action(async (opts) => {
   const cwd = process.cwd();
   const bin = findLocalBin(cwd);
   if (!bin) {
@@ -732,85 +827,86 @@ program.command("healthcheck").description(
     process.exit(1);
   }
   const mcpPath = join3(cwd, ".mcp.json");
-  if (existsSync3(mcpPath)) {
+  if (existsSync3(mcpPath) && !opts.json) {
     const data = readJsonSafe(mcpPath);
     const entries = data?.mcpServers && typeof data.mcpServers === "object" ? Object.entries(data.mcpServers) : [];
     const fragile = entries.filter(([, e]) => isNpxForm(e)).map(([k]) => k);
     if (fragile.length > 0) {
-      console.warn(
-        `\u26A0\uFE0F  .mcp.json uses the fragile npx-@latest form for: ${fragile.join(", ")}`
-      );
+      console.warn(`\u26A0\uFE0F  .mcp.json uses the fragile npx-@latest form for: ${fragile.join(", ")}`);
       console.warn(`   Rewrite to the stable form:`);
       console.warn(`     npx --no @theglitchking/semantic-memory normalize-config`);
     }
   }
-  const r = spawnSync("node", [bin, "--version"], { cwd, stdio: "pipe", timeout: 15e3 });
-  if (r.status === 0) {
-    console.log(`\u2713 local install starts cleanly (v${r.stdout?.toString().trim()})`);
-    process.exit(0);
-  }
-  const stderr = r.stderr?.toString() ?? "";
-  if (stderr.includes("ERR_MODULE_NOT_FOUND")) {
-    const match = stderr.match(/([\/~][^'"\s]*\/_npx\/[^\/'"\s]+)/);
-    if (match) {
-      const bad = match[1];
-      console.warn(`detected broken npx cache at ${bad} \u2014 clearing and retrying...`);
-      try {
-        rmSync(bad, { recursive: true, force: true });
-      } catch {
-      }
-      const r2 = spawnSync("node", [bin, "--version"], { cwd, stdio: "pipe", timeout: 15e3 });
-      if (r2.status === 0) {
-        console.log(`\u2713 cleared npx cache and verified (v${r2.stdout?.toString().trim()})`);
-        process.exit(0);
-      }
-      console.error(`retry still failed:
-${r2.stderr?.toString() || ""}`);
+  let smokeOk = false;
+  let smokeVersion = "";
+  {
+    const r = spawnSync("node", [bin, "--version"], { cwd, stdio: "pipe", timeout: 15e3 });
+    if (r.status === 0) {
+      smokeOk = true;
+      smokeVersion = r.stdout?.toString().trim() ?? "";
     } else {
-      console.error(`ERR_MODULE_NOT_FOUND but could not locate offending cache path in the error.`);
+      const stderr = r.stderr?.toString() ?? "";
+      if (stderr.includes("ERR_MODULE_NOT_FOUND")) {
+        const match = stderr.match(/([\/~][^'"\s]*\/_npx\/[^\/'"\s]+)/);
+        if (match) {
+          const bad = match[1];
+          if (!opts.json) console.warn(`detected broken npx cache at ${bad} \u2014 clearing and retrying...`);
+          try {
+            rmSync(bad, { recursive: true, force: true });
+          } catch {
+          }
+          const r2 = spawnSync("node", [bin, "--version"], { cwd, stdio: "pipe", timeout: 15e3 });
+          if (r2.status === 0) {
+            smokeOk = true;
+            smokeVersion = r2.stdout?.toString().trim() ?? "";
+          } else if (!opts.json) {
+            console.error(`retry still failed:
+${r2.stderr?.toString() || ""}`);
+          }
+        }
+      }
+      if (!smokeOk && !opts.json && stderr) console.error(stderr);
     }
   }
-  if (stderr) console.error(stderr);
-  if (r.status !== 0) {
-    console.error(`local install failed (exit ${r.status})`);
-    process.exit(1);
+  if (smokeOk && !opts.json) console.log(`\u2713 local install starts cleanly (v${smokeVersion})`);
+  const { runHealthcheck, formatDriftBanner, filterToDrift } = await import("../healthcheck-IMB47LZE.js");
+  const vaultCandidate = join3(cwd, ".claude", ".vault");
+  const vaultPath = existsSync3(vaultCandidate) ? vaultCandidate : void 0;
+  let result = await runHealthcheck({ projectRoot: cwd, vaultPath, tier: opts.fast ? "fast" : "all", force: true });
+  let fixOutcomes = [];
+  let plan = { fixes: [], skipped: [] };
+  if (opts.fix) {
+    plan = planFixes(filterToDrift(result));
+    if (plan.fixes.length > 0) {
+      fixOutcomes = await executeFixes(cwd, plan.fixes);
+      result = await runHealthcheck({ projectRoot: cwd, vaultPath, tier: opts.fast ? "fast" : "all", force: true });
+    }
   }
-});
-var driftHealthcheckActionPostprocess = async (opts) => {
-  try {
-    const { runHealthcheck, formatDriftBanner } = await import("../healthcheck-E4GI5RMZ.js");
-    const projectRoot = process.cwd();
-    const vaultCandidate = join3(projectRoot, ".claude", ".vault");
-    const vaultPath = existsSync3(vaultCandidate) ? vaultCandidate : void 0;
-    const result = await runHealthcheck({
-      projectRoot,
-      vaultPath,
-      tier: opts.fast ? "fast" : "all",
-      force: true
-    });
-    if (opts.json) {
-      console.log(JSON.stringify(result, null, 2));
-      return;
+  if (opts.json) {
+    console.log(JSON.stringify({ smoke: { ok: smokeOk, version: smokeVersion }, result, fix: opts.fix ? { plan, outcomes: fixOutcomes } : void 0 }, null, 2));
+  } else {
+    if (opts.fix) {
+      if (fixOutcomes.length === 0 && plan.skipped.length === 0) {
+        console.log(`
+\u2713 nothing to fix`);
+      } else {
+        console.log(`
+--fix applied ${fixOutcomes.filter((o) => o.status === "fixed").length}/${fixOutcomes.length} action(s):`);
+        for (const o of fixOutcomes) console.log(`  ${o.status === "fixed" ? "\u2713" : "\u2717"} ${o.action} (${o.check}) \u2014 ${o.detail}`);
+        for (const s of plan.skipped) console.log(`  \u2022 skipped ${s.check} \u2014 ${s.reason}`);
+      }
     }
     const banner = formatDriftBanner(result);
     if (banner) {
       console.log("");
       console.log(banner);
     } else {
-      console.log("");
-      console.log(`\u2713 no drift detected (${result.findings.length} checks ran in ${result.duration_ms}ms)`);
+      console.log(`
+\u2713 no drift detected (${result.findings.length} checks ran in ${result.duration_ms}ms)`);
     }
-  } catch (err) {
-    console.error(`drift check threw: ${err?.message ?? err}`);
   }
-};
-var healthcheckCmd = program.commands.find((c) => c.name() === "healthcheck");
-if (healthcheckCmd) {
-  healthcheckCmd.hook("postAction", async (thisCmd) => {
-    const opts = thisCmd.opts();
-    await driftHealthcheckActionPostprocess({ fast: !!opts.fast, json: !!opts.json });
-  });
-}
+  process.exit(smokeOk ? 0 : 1);
+});
 function parseAgent(input) {
   const a = input.toLowerCase();
   if (!SKILL_BUNDLER_AGENTS.includes(a)) {
@@ -899,5 +995,109 @@ ${result.conflicts.length} conflict${result.conflicts.length === 1 ? "" : "s"} d
     process.exit(1);
   }
 });
+program.command("decay-config").description("Print the active confidence-decay config (shipped defaults + any vault.schema.yml override).").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { loadDecayConfig, DEFAULT_DECAY_CONFIG } = await import("../decay-ELJUKVQG.js");
+  const cfg = loadDecayConfig(resolve2(opts.notes));
+  const source = JSON.stringify(cfg) === JSON.stringify(DEFAULT_DECAY_CONFIG) ? "defaults" : "vault.schema.yml (overridden)";
+  console.log(JSON.stringify({ source, config: cfg }, null, 2));
+  process.exit(0);
+});
+program.command("decay-trace <notePath>").description("Show the decay calculation for one note: type, last_verified, age, half-life, evergreen, multiplier.").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (notePath, opts) => {
+  const { loadDecayConfig, computeDecay, normalizeVerifiedDate } = await import("../decay-ELJUKVQG.js");
+  const matter = (await import("gray-matter")).default;
+  const abs = resolve2(opts.notes, notePath);
+  if (!existsSync3(abs)) {
+    console.error(`note not found: ${abs}`);
+    process.exit(1);
+  }
+  const { data: fm } = matter(readFileSync(abs, "utf8"));
+  const lastVerified = normalizeVerifiedDate(fm.last_verified);
+  const d = computeDecay({
+    type: typeof fm.type === "string" ? fm.type : void 0,
+    last_verified: lastVerified,
+    evergreen: fm.evergreen === true,
+    config: loadDecayConfig(resolve2(opts.notes))
+  });
+  console.log(
+    JSON.stringify(
+      {
+        path: notePath,
+        type: fm.type ?? null,
+        last_verified: lastVerified ?? null,
+        evergreen: fm.evergreen === true,
+        multiplier: d.multiplier,
+        age_days: Math.round(d.age_days),
+        effective_half_life: d.effective_half_life,
+        reason: d.reason
+      },
+      null,
+      2
+    )
+  );
+  process.exit(0);
+});
+var lexiconCmd = program.command("lexicon").description("Manage the learned human\u2192artifact lexicon (aliases).");
+lexiconCmd.command("list").description("List all aliases in the lexicon.").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { loadLexiconCache } = await import("../lexicon-5PXQEMUF.js");
+  console.log(JSON.stringify(await loadLexiconCache(resolve2(opts.notes)), null, 2));
+  process.exit(0);
+});
+lexiconCmd.command("compile").description("Rebuild the derived lexicon cache from the lexicon/ notes.").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { compileLexicon } = await import("../lexicon-5PXQEMUF.js");
+  const entries = await compileLexicon(resolve2(opts.notes));
+  console.log(`compiled ${entries.length} alias(es)`);
+  process.exit(0);
+});
+lexiconCmd.command("add <canonical> <phrases...>").description("Upsert an alias: a canonical target and the human phrases that refer to it.").requiredOption("--notes <path>", "Path to markdown notes directory").option("--authored", "Mark as human-authored (default: learned)").action(async (canonical, phrases, opts) => {
+  const { addAlias } = await import("../lexicon-5PXQEMUF.js");
+  const r = await addAlias(resolve2(opts.notes), { canonical, phrases, source: opts.authored ? "authored" : "learned" });
+  console.log(JSON.stringify(r, null, 2));
+  process.exit(0);
+});
+var dossierCmd = program.command("dossier").description("Manage entity dossiers \u2014 per-component living notes (purpose / failure modes / knobs / incident log / current state).");
+dossierCmd.command("init <entity>").description("Scaffold a dossier for an entity (no-op if one already exists). Optionally seed aliases and provenance.").requiredOption("--notes <path>", "Path to markdown notes directory").option("--alias <phrase...>", "Human phrase(s) for this entity \u2014 fed to the lexicon compiler").option("--seeded-from <ref>", "Provenance of the scaffold (e.g. a babel-fish project-map entry)").action(async (entity, opts) => {
+  const { initDossier } = await import("../dossier-2UG724LB.js");
+  const r = await initDossier(resolve2(opts.notes), entity, { aliases: opts.alias, seeded_from: opts.seededFrom });
+  console.log(JSON.stringify(r, null, 2));
+  process.exit(0);
+});
+dossierCmd.command("list").description("List all dossiers with their entity, aliases, and current state.").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { listDossiers } = await import("../dossier-2UG724LB.js");
+  console.log(JSON.stringify(await listDossiers(resolve2(opts.notes)), null, 2));
+  process.exit(0);
+});
+var profileCmd = program.command("profile").description("Manage the speaker profile \u2014 how THIS human communicates (severity calibration, chronic omissions, verbosity, shorthand).");
+profileCmd.command("init").description("Scaffold profile/speaker.md with the fixed sections (no-op if it exists).").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { initSpeakerProfile } = await import("../profile-LXUEF7TX.js");
+  const r = await initSpeakerProfile(resolve2(opts.notes));
+  console.log(JSON.stringify(r, null, 2));
+  process.exit(0);
+});
+profileCmd.command("show").description("Print the speaker profile's injection head (the capped, placeholder-stripped view).").requiredOption("--notes <path>", "Path to markdown notes directory").action(async (opts) => {
+  const { readSpeakerProfile } = await import("../profile-LXUEF7TX.js");
+  const p = await readSpeakerProfile(resolve2(opts.notes));
+  console.log(p ? p.head || "(profile is empty \u2014 only placeholders)" : "(no speaker profile \u2014 run `profile init`)");
+  process.exit(0);
+});
+program.command("selection-stats").description("Summarize the local selection log: searches, selections, most-cited notes, and retrieved-but-never-cited notes.").requiredOption("--notes <path>", "Path to markdown notes directory").option("--json", "Emit raw JSON instead of a human summary").action(async (opts) => {
+  const { computeSelectionStats, selectionLogPath } = await import("../telemetry-GB2TEHVE.js");
+  const stats = await computeSelectionStats(resolve2(opts.notes));
+  if (opts.json) {
+    console.log(JSON.stringify(stats, null, 2));
+    process.exit(0);
+  }
+  console.log(`Selection log: ${selectionLogPath(resolve2(opts.notes))}`);
+  console.log(`  searches:   ${stats.searches}`);
+  console.log(`  selections: ${stats.selections}`);
+  const topCited = Object.entries(stats.citedPaths).sort((a, b) => b[1] - a[1]).slice(0, 10);
+  if (topCited.length) {
+    console.log(`  most cited:`);
+    for (const [p, n] of topCited) console.log(`    ${n}\xD7  ${p}`);
+  }
+  if (stats.retrievedNeverCited.length) {
+    console.log(`  retrieved but never cited (${stats.retrievedNeverCited.length}): ${stats.retrievedNeverCited.slice(0, 10).join(", ")}${stats.retrievedNeverCited.length > 10 ? " \u2026" : ""}`);
+  }
+  process.exit(0);
+});
 program.parse();
 //# sourceMappingURL=index.js.map