@goondocks/myco 0.18.0 → 0.18.1

package/dist/{chunk-JDI4DPWD.js → chunk-C3EGL5JX.js}

@@ -12,11 +12,13 @@ import {
 } from "./chunk-NI23QCHB.js";
 import {
   getSpore,
-  listSporeIdsSince
-} from "./chunk-7OYXB2NM.js";
+  listSporeIdsSince,
+  listSpores
+} from "./chunk-TZAXQKO6.js";
 import {
-  getSession
-} from "./chunk-U7GJTVSX.js";
+  getSession,
+  listSessions
+} from "./chunk-RIDSOQDR.js";
 import {
   getTeamMachineId,
   syncRow
@@ -169,6 +171,10 @@ function errorMessage(err) {
   }
 }
 
+// src/agent/instruction-builders.ts
+import { readFileSync } from "fs";
+import { resolve } from "path";
+
 // src/db/queries/skill-candidates.ts
 var DEFAULT_CONFIDENCE = 0;
 var DEFAULT_STATUS = "identified";
@@ -182,6 +188,7 @@ var CANDIDATE_COLUMNS = [
   "status",
   "source_ids",
   "skill_id",
+  "supersedes",
   "approved_at",
   "created_at",
   "updated_at",
@@ -199,6 +206,7 @@ function toCandidateRow(row) {
     status: row.status,
     source_ids: row.source_ids ?? "[]",
     skill_id: row.skill_id ?? null,
+    supersedes: row.supersedes ?? null,
     approved_at: row.approved_at ?? null,
     created_at: row.created_at,
     updated_at: row.updated_at,
@@ -230,11 +238,11 @@ function insertCandidate(data) {
   db.prepare(
     `INSERT INTO skill_candidates (
        id, agent_id, machine_id, topic, rationale,
-       confidence, status, source_ids, skill_id, approved_at,
+       confidence, status, source_ids, skill_id, supersedes, approved_at,
        created_at, updated_at
      ) VALUES (
        ?, ?, ?, ?, ?,
-       ?, ?, ?, ?, ?,
+       ?, ?, ?, ?, ?, ?,
        ?, ?
      )`
   ).run(
@@ -247,6 +255,7 @@ function insertCandidate(data) {
     data.status ?? DEFAULT_STATUS,
     data.source_ids ?? "[]",
     data.skill_id ?? null,
+    data.supersedes ?? null,
     data.approved_at ?? null,
     data.created_at,
     data.updated_at
@@ -296,6 +305,7 @@ function updateCandidate(id, updates) {
     status: "status",
     source_ids: "source_ids",
     skill_id: "skill_id",
+    supersedes: "supersedes",
     approved_at: "approved_at",
     updated_at: "updated_at"
   };
@@ -556,69 +566,357 @@ function deleteSkillRecordCascade(idOrName) {
   return { id: record.id, name: record.name };
 }
 
-// src/db/queries/skill-lineage.ts
-var LINEAGE_COLUMNS = [
+// src/db/queries/digest-extracts.ts
+var EXTRACT_COLUMNS = [
   "id",
-  "skill_id",
-  "generation",
-  "action",
-  "rationale",
-  "source_ids_added",
-  "content_snapshot",
-  "created_at"
+  "agent_id",
+  "tier",
+  "content",
+  "substrate_hash",
+  "generated_at",
+  "machine_id",
+  "synced_at"
 ];
-var SELECT_COLUMNS3 = LINEAGE_COLUMNS.join(", ");
-function toLineageRow(row) {
+var SELECT_COLUMNS3 = EXTRACT_COLUMNS.join(", ");
+function toDigestExtractRow(row) {
   return {
     id: row.id,
-    skill_id: row.skill_id,
-    generation: row.generation,
-    action: row.action,
-    rationale: row.rationale,
-    source_ids_added: row.source_ids_added ?? "[]",
-    content_snapshot: row.content_snapshot,
-    created_at: row.created_at
+    agent_id: row.agent_id,
+    tier: row.tier,
+    content: row.content,
+    substrate_hash: row.substrate_hash ?? null,
+    generated_at: row.generated_at,
+    machine_id: row.machine_id ?? "local",
+    synced_at: row.synced_at ?? null
   };
 }
-function insertLineage(data) {
+function upsertDigestExtract(data) {
   const db = getDatabase();
   db.prepare(
-    `INSERT INTO skill_lineage (
-       id, skill_id, generation, action, rationale,
-       source_ids_added, content_snapshot, created_at
-     ) VALUES (
-       ?, ?, ?, ?, ?,
-       ?, ?, ?
-     )`
-  ).run(
-    data.id,
-    data.skill_id,
-    data.generation,
-    data.action,
-    data.rationale,
-    data.source_ids_added ?? "[]",
-    data.content_snapshot,
-    data.created_at
-  );
-  return toLineageRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS3} FROM skill_lineage WHERE id = ?`).get(data.id)
-  );
+    `INSERT INTO digest_extracts (agent_id, tier, content, generated_at)
+     VALUES (?, ?, ?, ?)
+     ON CONFLICT (agent_id, tier) DO UPDATE SET
+       content = EXCLUDED.content,
+       generated_at = EXCLUDED.generated_at`
+  ).run(data.agent_id, data.tier, data.content, data.generated_at);
+  const row = db.prepare(
+    `SELECT ${SELECT_COLUMNS3} FROM digest_extracts WHERE agent_id = ? AND tier = ?`
+  ).get(data.agent_id, data.tier);
+  return toDigestExtractRow(row);
 }
-function listLineageForSkill(skillId, limit = 50) {
+function getDigestExtract(agentId, tier) {
   const db = getDatabase();
+  const row = db.prepare(
+    `SELECT ${SELECT_COLUMNS3} FROM digest_extracts
+     WHERE agent_id = ? AND tier = ?`
+  ).get(agentId, tier);
+  if (!row) return null;
+  return toDigestExtractRow(row);
+}
+function listDigestExtracts(agentId) {
+  const db = getDatabase();
+  const tierPlaceholders = DIGEST_TIERS.map(() => "?").join(", ");
   const rows = db.prepare(
     `SELECT ${SELECT_COLUMNS3}
-     FROM skill_lineage
-     WHERE skill_id = ?
-     ORDER BY generation DESC
-     LIMIT ?`
-  ).all(skillId, limit);
-  return rows.map(toLineageRow);
+     FROM digest_extracts
+     WHERE agent_id = ? AND tier IN (${tierPlaceholders})
+     ORDER BY tier ASC`
+  ).all(agentId, ...DIGEST_TIERS);
+  return rows.map(toDigestExtractRow);
+}
+
+// src/db/queries/agent-state.ts
+var STATE_COLUMNS = [
+  "agent_id",
+  "key",
+  "value",
+  "updated_at"
+];
+var SELECT_COLUMNS4 = STATE_COLUMNS.join(", ");
+function toAgentStateRow(row) {
+  return {
+    agent_id: row.agent_id,
+    key: row.key,
+    value: row.value,
+    updated_at: row.updated_at
+  };
+}
+function getState(agentId, key) {
+  const db = getDatabase();
+  const row = db.prepare(
+    `SELECT ${SELECT_COLUMNS4} FROM agent_state WHERE agent_id = ? AND key = ?`
+  ).get(agentId, key);
+  if (!row) return null;
+  return toAgentStateRow(row);
+}
+function setState(agentId, key, value, updatedAt) {
+  const db = getDatabase();
+  db.prepare(
+    `INSERT INTO agent_state (agent_id, key, value, updated_at)
+     VALUES (?, ?, ?, ?)
+     ON CONFLICT (agent_id, key) DO UPDATE SET
+       value      = EXCLUDED.value,
+       updated_at = EXCLUDED.updated_at`
+  ).run(agentId, key, value, updatedAt);
+  return toAgentStateRow(
+    db.prepare(`SELECT ${SELECT_COLUMNS4} FROM agent_state WHERE agent_id = ? AND key = ?`).get(agentId, key)
+  );
+}
+function getStatesForAgent(agentId) {
+  const db = getDatabase();
+  const rows = db.prepare(
+    `SELECT ${SELECT_COLUMNS4}
+     FROM agent_state
+     WHERE agent_id = ?
+     ORDER BY key ASC`
+  ).all(agentId);
+  return rows.map(toAgentStateRow);
+}
+
+// src/agent/tools/skill-validator.ts
+var MAX_SKILL_LINES = 800;
+var REQUIRED_FRONTMATTER_FIELDS = ["name", "description", "managed_by", "user-invocable", "allowed-tools"];
+var PROTECTED_FRONTMATTER_FIELDS = ["user-invocable", "allowed-tools"];
+var ALLOWED_CLAUDE_CODE_TOOLS = /* @__PURE__ */ new Set([
+  "Read",
+  "Edit",
+  "Write",
+  "MultiEdit",
+  "Bash",
+  "Grep",
+  "Glob",
+  "NotebookRead",
+  "NotebookEdit",
+  "WebFetch",
+  "WebSearch",
+  "Task",
+  "TodoWrite"
+]);
+function extractFrontmatterField(content, field) {
+  const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
+  if (!fmMatch) return void 0;
+  const fm = fmMatch[1];
+  const match = fm.match(new RegExp(`^${field}:\\s*(.+)$`, "m"));
+  if (match) return match[1].trim();
+  const blockMatch = fm.match(new RegExp(`^${field}:\\s*$`, "m"));
+  if (blockMatch) {
+    const startIdx = fm.indexOf(blockMatch[0]) + blockMatch[0].length;
+    const remaining = fm.slice(startIdx);
+    const items = [];
+    for (const line of remaining.split("\n")) {
+      const itemMatch = line.match(/^\s+-\s+(.+)$/);
+      if (!itemMatch) break;
+      items.push(itemMatch[1].trim());
+    }
+    if (items.length > 0) return items.join(", ");
+  }
+  return void 0;
+}
+function parseAllowedTools(rawValue) {
+  if (!rawValue) return null;
+  let stripped = rawValue.trim();
+  if (stripped.length === 0) return null;
+  if (stripped.startsWith("[") && stripped.endsWith("]")) {
+    stripped = stripped.slice(1, -1).trim();
+  }
+  if (stripped.length === 0) return null;
+  const parts = stripped.split(",").map((s) => s.trim().replace(/^['"]|['"]$/g, "")).filter((s) => s.length > 0);
+  if (parts.length === 0) return null;
+  const sentinels = /* @__PURE__ */ new Set(["None", "none", "null", "Null", "~"]);
+  if (parts.some((p) => sentinels.has(p))) return null;
+  return parts;
+}
+function stemToken(word) {
+  let w = word;
+  if (w.length > 5 && w.endsWith("ing")) w = w.slice(0, -3);
+  else if (w.length > 5 && w.endsWith("ed")) w = w.slice(0, -2);
+  if (w.length > 4 && w.endsWith("s")) w = w.slice(0, -1);
+  if (w.length > 4 && w.endsWith("e")) w = w.slice(0, -1);
+  return w;
+}
+var STOPWORDS = /* @__PURE__ */ new Set([
+  "the",
+  "a",
+  "an",
+  "and",
+  "or",
+  "but",
+  "is",
+  "are",
+  "was",
+  "were",
+  "be",
+  "been",
+  "being",
+  "have",
+  "has",
+  "had",
+  "do",
+  "does",
+  "did",
+  "will",
+  "would",
+  "should",
+  "could",
+  "may",
+  "might",
+  "must",
+  "can",
+  "this",
+  "that",
+  "these",
+  "those",
+  "with",
+  "from",
+  "into",
+  "onto",
+  "for",
+  "when",
+  "where",
+  "which",
+  "what",
+  "who",
+  "how",
+  "why",
+  "use",
+  "uses",
+  "used",
+  "using",
+  "not",
+  "also",
+  "than",
+  "then",
+  "ensure",
+  "ensures",
+  "make",
+  "makes"
+]);
+function tokenSet(text) {
+  return new Set(
+    text.toLowerCase().replace(/[^a-z0-9_\s]/g, " ").split(/\s+/).filter((w) => w.length >= 4 && !STOPWORDS.has(w)).map(stemToken)
+  );
+}
+function intersectionSize(a, b) {
+  let count = 0;
+  for (const token of a) {
+    if (b.has(token)) count++;
+  }
+  return count;
+}
+function descriptionSimilarity(a, b) {
+  const aTokens = tokenSet(a);
+  const bTokens = tokenSet(b);
+  if (aTokens.size === 0 || bTokens.size === 0) return 0;
+  const intersection = intersectionSize(aTokens, bTokens);
+  const union = aTokens.size + bTokens.size - intersection;
+  return union === 0 ? 0 : intersection / union;
+}
+function topicOverlapSimilarity(a, b, minTokens = 3) {
+  const aTokens = tokenSet(a);
+  const bTokens = tokenSet(b);
+  if (aTokens.size < minTokens || bTokens.size < minTokens) return 0;
+  const intersection = intersectionSize(aTokens, bTokens);
+  const smaller = Math.min(aTokens.size, bTokens.size);
+  return smaller === 0 ? 0 : intersection / smaller;
+}
+var DESCRIPTION_DUPLICATE_THRESHOLD = 0.4;
+var TOPIC_OVERLAP_THRESHOLD = 0.6;
+function checkFrontmatterPreservation(existing, incoming) {
+  const violations = [];
+  for (const field of PROTECTED_FRONTMATTER_FIELDS) {
+    const oldValue = extractFrontmatterField(existing, field);
+    const newValue = extractFrontmatterField(incoming, field);
+    if (oldValue === void 0 || newValue === void 0) continue;
+    if (field === "allowed-tools") {
+      const oldParsed = parseAllowedTools(oldValue);
+      const newParsed = parseAllowedTools(newValue);
+      if (oldParsed && newParsed) {
+        const oldSet = new Set(oldParsed);
+        const newSet = new Set(newParsed);
+        const changed = oldSet.size !== newSet.size || [...oldSet].some((t) => !newSet.has(t));
+        if (changed) {
+          violations.push(`${field}: was [${oldParsed.join(", ")}], changed to [${newParsed.join(", ")}]`);
+        }
+        continue;
+      }
+    }
+    if (oldValue !== newValue) {
+      violations.push(`${field}: was "${oldValue}", changed to "${newValue}"`);
+    }
+  }
+  const oldDesc = extractFrontmatterField(existing, "description");
+  const newDesc = extractFrontmatterField(incoming, "description");
+  if (oldDesc && newDesc && newDesc.length < oldDesc.length * 0.9) {
+    violations.push(
+      `description shortened from ${oldDesc.length} to ${newDesc.length} chars (${Math.round((1 - newDesc.length / oldDesc.length) * 100)}% reduction). Descriptions are the primary triggering mechanism \u2014 do not shorten them.`
+    );
+  }
+  return violations;
+}
+function validateSkillContent(content, dirName) {
+  const issues = [];
+  const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
+  if (!fmMatch) {
+    issues.push("Missing YAML frontmatter (must start with --- and end with ---)");
+    return issues;
+  }
+  const frontmatter = fmMatch[1];
+  for (const field of REQUIRED_FRONTMATTER_FIELDS) {
+    if (!frontmatter.includes(`${field}:`)) {
+      issues.push(`Missing required frontmatter field: ${field}`);
+    }
+  }
+  const nameMatch = frontmatter.match(/^name:\s*(.+)$/m);
+  if (nameMatch && !nameMatch[1].trim().startsWith("myco:")) {
+    issues.push(`Skill name must start with "myco:" prefix. Got: "${nameMatch[1].trim()}"`);
+  }
+  const managedMatch = frontmatter.match(/^managed_by:\s*(.+)$/m);
+  if (managedMatch && managedMatch[1].trim() !== "myco") {
+    issues.push(`managed_by must be "myco". Got: "${managedMatch[1].trim()}"`);
+  }
+  const rawAllowedTools = extractFrontmatterField(content, "allowed-tools");
+  if (rawAllowedTools) {
+    const rawValue = rawAllowedTools;
+    if (rawValue.includes("vault_")) {
+      issues.push(
+        "allowed-tools contains vault agent tool names (vault_*). Skills run in Claude Code sessions -- use Claude Code tool names instead: Read, Edit, Write, Bash, Grep, Glob"
+      );
+    } else {
+      const parsed = parseAllowedTools(rawValue);
+      if (parsed === null) {
+        issues.push(
+          `allowed-tools value is malformed or empty: "${rawValue}". Provide a comma-separated list of Claude Code tools, e.g. "Read, Edit, Write, Bash, Grep, Glob". Use the narrowest set the skill actually needs.`
+        );
+      } else {
+        const unknown = parsed.filter((t) => !ALLOWED_CLAUDE_CODE_TOOLS.has(t));
+        if (unknown.length > 0) {
+          issues.push(
+            `allowed-tools contains unknown tool name(s): ${unknown.join(", ")}. Valid Claude Code tools: ${[...ALLOWED_CLAUDE_CODE_TOOLS].join(", ")}.`
+          );
+        }
+      }
+    }
+  }
+  const listToolLines = frontmatter.match(/^\s+-\s+vault_\w+/gm);
+  if (listToolLines) {
+    issues.push(
+      "allowed-tools contains vault agent tool names (vault_*). Skills run in Claude Code sessions -- use Claude Code tool names instead: Read, Edit, Write, Bash, Grep, Glob"
+    );
+  }
+  const lineCount = content.split("\n").length;
+  if (lineCount > MAX_SKILL_LINES) {
+    issues.push(`Skill is ${lineCount} lines (max ${MAX_SKILL_LINES})`);
+  }
+  return issues;
 }
 
 // src/agent/instruction-builders.ts
 var SKILL_GENERATE_TASK = "skill-generate";
 var SKILL_EVOLVE_TASK = "skill-evolve";
+var SKILL_SURVEY_TASK = "skill-survey";
+var SURVEY_MAX_WISDOM_SPORES = 30;
+var SURVEY_MAX_SESSIONS = 15;
+var SURVEY_WATERMARK_KEY = "skill-survey-watermark";
 function buildSkillGenerateInstruction() {
   const candidates = listCandidates({ status: "approved", limit: 1 });
   if (candidates.length === 0) return void 0;
@@ -661,9 +959,103 @@ function buildSkillGenerateInstruction() {
     context: { candidate_id: c.id }
   };
 }
+function buildSkillSurveyInstruction(agentId) {
+  const now = epochSeconds();
+  const watermarkState = getState(agentId, SURVEY_WATERMARK_KEY);
+  const watermarkEpoch = watermarkState ? Number(watermarkState.value) : 0;
+  const sinceFilter = watermarkEpoch > 0 ? { since: watermarkEpoch } : {};
+  const parts = [
+    "## Pre-assembled Vault Context",
+    "",
+    `Survey watermark: ${watermarkEpoch === 0 ? "first run (full scan)" : new Date(watermarkEpoch * 1e3).toISOString()}`,
+    ""
+  ];
+  const digests = listDigestExtracts(agentId);
+  if (digests.length > 0) {
+    const smallest = digests.reduce((a, b) => a.tier < b.tier ? a : b);
+    parts.push("### Digest");
+    parts.push(`**Tier ${smallest.tier}** (${smallest.content.length} chars):`);
+    parts.push(smallest.content);
+    parts.push("");
+  }
+  const wisdomSpores = listSpores({
+    observation_type: "wisdom",
+    limit: SURVEY_MAX_WISDOM_SPORES,
+    ...sinceFilter
+  });
+  if (wisdomSpores.length > 0) {
+    parts.push(`### Wisdom Spores (${wisdomSpores.length})`);
+    for (const s of wisdomSpores) {
+      parts.push(`- **${s.id}** (importance ${s.importance}): ${s.content.slice(0, 300)}`);
+    }
+    parts.push("");
+  }
+  const decisions = listSpores({
+    observation_type: "decision",
+    limit: 20,
+    ...sinceFilter
+  });
+  const gotchas = listSpores({
+    observation_type: "gotcha",
+    limit: 10,
+    ...sinceFilter
+  });
+  if (decisions.length > 0 || gotchas.length > 0) {
+    parts.push(`### Decisions (${decisions.length}) & Gotchas (${gotchas.length})`);
+    for (const s of [...decisions, ...gotchas]) {
+      parts.push(`- **${s.observation_type}** ${s.id}: ${s.content.slice(0, 200)}`);
+    }
+    parts.push("");
+  }
+  const sessions = listSessions({
+    limit: SURVEY_MAX_SESSIONS,
+    ...sinceFilter
+  });
+  if (sessions.length > 0) {
+    parts.push(`### Recent Sessions (${sessions.length})`);
+    for (const s of sessions) {
+      parts.push(`- **${s.id}**: ${s.title ?? "(untitled)"} \u2014 ${(s.summary ?? "").slice(0, 200)}`);
+    }
+    parts.push("");
+  }
+  const activeSkills = listSkillRecords({ status: "active", limit: 100 });
+  parts.push(`### Active Skills (${activeSkills.length})`);
+  for (const s of activeSkills) {
+    parts.push(`- **${s.name}**: ${s.description.slice(0, 150)}`);
+  }
+  parts.push("");
+  setState(agentId, SURVEY_WATERMARK_KEY, String(now), now);
+  return { instruction: parts.join("\n") };
+}
 var SKILL_EVOLVE_DEFAULT_ASSESS_INTERVAL_HOURS = 24;
-var SKILL_EVOLVE_DEFAULT_MAX_SKILLS_PER_RUN = 5;
-function buildSkillEvolveInstruction(params) {
+var SKILL_EVOLVE_DEFAULT_MAX_SKILLS_PER_RUN = 8;
+var MIN_SECTIONS_FOR_STANDALONE = 2;
+function extractHeadings(content) {
+  const bodyMatch = content.match(/^---[\s\S]*?---\n([\s\S]*)$/);
+  const body = bodyMatch ? bodyMatch[1] : content;
+  return body.split("\n").filter((line) => line.startsWith("## ")).map((line) => line.slice(3).trim());
+}
+function headingOverlap(headingsA, headingsB) {
+  if (headingsA.length === 0 || headingsB.length === 0) return { score: 0, shared: [] };
+  const tokenize = (h) => new Set(
+    h.toLowerCase().replace(/[^a-z0-9\s]/g, " ").split(/\s+/).filter((w) => w.length >= 4)
+  );
+  const shared = [];
+  for (const a of headingsA) {
+    const aTokens = tokenize(a);
+    for (const b of headingsB) {
+      const bTokens = tokenize(b);
+      const intersection = [...aTokens].filter((t) => bTokens.has(t)).length;
+      const union = (/* @__PURE__ */ new Set([...aTokens, ...bTokens])).size;
+      if (union > 0 && intersection / union >= 0.5) {
+        shared.push(`"${a}" ~ "${b}"`);
+      }
+    }
+  }
+  const smaller = Math.min(headingsA.length, headingsB.length);
+  return { score: smaller > 0 ? shared.length / smaller : 0, shared };
+}
+function buildSkillEvolveInstruction(params, projectRoot, similarityProvider) {
   const assessIntervalHours = Number(params?.assess_interval_hours ?? SKILL_EVOLVE_DEFAULT_ASSESS_INTERVAL_HOURS);
   const maxSkillsPerRun = Number(params?.max_skills_per_run ?? SKILL_EVOLVE_DEFAULT_MAX_SKILLS_PER_RUN);
   const now = epochSeconds();
@@ -682,14 +1074,11 @@ function buildSkillEvolveInstruction(params) {
     if (lastAssessedAt > 0 && now - lastAssessedAt < intervalSeconds) continue;
     const newSporeIds = listSporeIdsSince(knowledgeWatermark, 10);
     if (newSporeIds.length === 0) continue;
-    const lineage = listLineageForSkill(skill.id, 1);
-    if (lineage.length === 0) continue;
     needsAssessment.push({
       id: skill.id,
       name: skill.name,
       generation: skill.generation,
       description: skill.description,
-      contentSnapshot: lineage[0].content_snapshot,
       newSporeIds
     });
     if (needsAssessment.length >= maxSkillsPerRun) {
@@ -699,6 +1088,48 @@ function buildSkillEvolveInstruction(params) {
   if (needsAssessment.length === 0) {
     return "No skills need assessment. All active skills are current or were recently assessed. Report skip via vault_report and finish.";
   }
+  const structures = [];
+  const skillHeadings = /* @__PURE__ */ new Map();
+  for (const skill of allSkills) {
+    let content = "";
+    if (projectRoot && skill.path) {
+      try {
+        content = readFileSync(resolve(projectRoot, skill.path), "utf-8");
+      } catch {
+      }
+    }
+    const headings = extractHeadings(content);
+    skillHeadings.set(skill.name, headings);
+    structures.push({
+      name: skill.name,
+      sectionCount: headings.length,
+      headings,
+      narrow: headings.length < MIN_SECTIONS_FOR_STANDALONE
+    });
+  }
+  const overlaps = [];
+  for (let i = 0; i < allSkills.length; i++) {
+    for (let j = i + 1; j < allSkills.length; j++) {
+      const a = allSkills[i];
+      const b = allSkills[j];
+      const descJaccard = descriptionSimilarity(a.description, b.description);
+      const aHeadings = skillHeadings.get(a.name) ?? [];
+      const bHeadings = skillHeadings.get(b.name) ?? [];
+      const ho = headingOverlap(aHeadings, bHeadings);
+      const descFlag = descJaccard >= DESCRIPTION_DUPLICATE_THRESHOLD * 0.75;
+      const headingFlag = ho.score >= 0.4;
+      if (!descFlag && !headingFlag) continue;
+      const verdict = descJaccard >= DESCRIPTION_DUPLICATE_THRESHOLD || ho.score >= 0.5 ? "potential-merge" : "potential-narrow";
+      overlaps.push({
+        skillA: a.name,
+        skillB: b.name,
+        descriptionJaccard: Math.round(descJaccard * 100) / 100,
+        headingOverlap: Math.round(ho.score * 100) / 100,
+        sharedHeadings: ho.shared,
+        verdict
+      });
+    }
+  }
   const parts = [
     `${needsAssessment.length} skill(s) need assessment.`,
     `assess_interval_hours: ${assessIntervalHours}`,
@@ -711,19 +1142,66 @@ function buildSkillEvolveInstruction(params) {
     parts.push(`id: ${skill.id}`);
     parts.push(`description: ${skill.description}`);
     parts.push(`new_spore_ids: ${JSON.stringify(skill.newSporeIds)}`);
+  }
+  parts.push("");
+  parts.push("## All Active Skills (for inventory analysis)");
+  for (const s of structures) {
+    const skill = allSkills.find((sk) => sk.name === s.name);
+    const narrowTag = s.narrow ? " **[NARROW \u2014 <2 sections]**" : "";
+    parts.push(`- **${skill.name}** (gen ${skill.generation}, ${s.sectionCount} sections${narrowTag}): ${skill.description.slice(0, 200)}`);
+    if (s.headings.length > 0) {
+      parts.push(`  Headings: ${s.headings.join(" | ")}`);
+    }
+  }
+  const narrowSkills = structures.filter((s) => s.narrow);
+  if (narrowSkills.length > 0) {
     parts.push("");
-    parts.push("### Current Content");
+    parts.push("## Mechanically Narrow Skills (<2 H2 sections)");
+    parts.push("These skills have insufficient section breadth for domain-level standalone status.");
+    parts.push("Determine which broader skill each should be absorbed into.");
+    for (const s of narrowSkills) {
+      parts.push(`- **${s.name}**: ${s.sectionCount} section(s). Headings: ${s.headings.length > 0 ? s.headings.join(" | ") : "(none)"}`);
+    }
+  }
+  if (overlaps.length > 0) {
     parts.push("");
-    parts.push(skill.contentSnapshot);
+    parts.push("## Pre-computed Token Overlap");
+    parts.push("Pairs flagged by description token similarity AND/OR heading overlap:");
+    for (const o of overlaps) {
+      parts.push(`- **${o.skillA}** <-> **${o.skillB}**: desc=${o.descriptionJaccard}, headings=${o.headingOverlap} (${o.verdict})`);
+      if (o.sharedHeadings.length > 0) {
+        parts.push(`  Shared headings: ${o.sharedHeadings.join("; ")}`);
+      }
+    }
+  }
+  if (similarityProvider) {
+    const idToName = new Map(allSkills.map((s) => [s.id, s.name]));
+    try {
+      const semanticPairs = similarityProvider.pairwiseSimilarity("skill_records", 0.65);
+      if (semanticPairs.length > 0) {
+        parts.push("");
+        parts.push("## Semantic Similarity (embedding cosine distance)");
+        parts.push("Pairs with cosine similarity >= 0.65. This is the STRONGEST overlap signal.");
+        parts.push("High similarity (>0.8) means the skills describe nearly identical procedures.");
+        for (const p of semanticPairs) {
+          const nameA = idToName.get(p.idA) ?? p.idA;
+          const nameB = idToName.get(p.idB) ?? p.idB;
+          parts.push(`- **${nameA}** <-> **${nameB}**: cosine=${p.similarity}`);
+        }
+      }
+    } catch {
+    }
   }
   return parts.join("\n");
 }
-function buildTaskInstruction(taskName, taskParams) {
+function buildTaskInstruction(taskName, taskParams, agentId, projectRoot, similarityProvider) {
   switch (taskName) {
     case SKILL_GENERATE_TASK:
       return buildSkillGenerateInstruction();
+    case SKILL_SURVEY_TASK:
+      return agentId ? buildSkillSurveyInstruction(agentId) : void 0;
     case SKILL_EVOLVE_TASK: {
-      const instruction = buildSkillEvolveInstruction(taskParams);
+      const instruction = buildSkillEvolveInstruction(taskParams, projectRoot, similarityProvider);
       return instruction ? { instruction } : void 0;
     }
     default:
@@ -731,7 +1209,7 @@ function buildTaskInstruction(taskName, taskParams) {
   }
 }
 function isInstructionRequiredTask(taskName) {
-  return taskName === SKILL_GENERATE_TASK || taskName === SKILL_EVOLVE_TASK;
+  return taskName === SKILL_GENERATE_TASK || taskName === SKILL_EVOLVE_TASK || taskName === SKILL_SURVEY_TASK;
 }
 
 // src/db/queries/runs.ts
@@ -753,7 +1231,7 @@ var RUN_COLUMNS = [
   "actions_taken",
   "error"
 ];
-var SELECT_COLUMNS4 = RUN_COLUMNS.join(", ");
+var SELECT_COLUMNS5 = RUN_COLUMNS.join(", ");
 function toRunRow(row) {
   return {
     id: row.id,
@@ -795,13 +1273,13 @@ function insertRun(data) {
     data.error ?? null
   );
   return toRunRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS4} FROM agent_runs WHERE id = ?`).get(data.id)
+    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`).get(data.id)
   );
 }
 function getRun(id) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS4} FROM agent_runs WHERE id = ?`
+    `SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`
   ).get(id);
   if (!row) return null;
   return toRunRow(row);
@@ -836,7 +1314,7 @@ function listRuns(options = {}) {
   const limit = options.limit ?? DEFAULT_LIST_LIMIT2;
   const offset = options.offset ?? 0;
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS4}
+    `SELECT ${SELECT_COLUMNS5}
      FROM agent_runs
      ${where}
      ORDER BY started_at DESC NULLS LAST
@@ -885,7 +1363,7 @@ function updateRunStatus(id, status, completion) {
   ).run(...params);
   if (info.changes === 0) return null;
   return toRunRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS4} FROM agent_runs WHERE id = ?`).get(id)
+    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`).get(id)
   );
 }
 function getRunningRunForTask(agentId, taskName) {
@@ -994,6 +1472,66 @@ function resolveRunConfig(agentId, requestedTask, vaultDir) {
   };
 }
 
+// src/db/queries/skill-lineage.ts
+var LINEAGE_COLUMNS = [
+  "id",
+  "skill_id",
+  "generation",
+  "action",
+  "rationale",
+  "source_ids_added",
+  "content_snapshot",
+  "created_at"
+];
+var SELECT_COLUMNS6 = LINEAGE_COLUMNS.join(", ");
+function toLineageRow(row) {
+  return {
+    id: row.id,
+    skill_id: row.skill_id,
+    generation: row.generation,
+    action: row.action,
+    rationale: row.rationale,
+    source_ids_added: row.source_ids_added ?? "[]",
+    content_snapshot: row.content_snapshot,
+    created_at: row.created_at
+  };
+}
+function insertLineage(data) {
+  const db = getDatabase();
+  db.prepare(
+    `INSERT INTO skill_lineage (
+       id, skill_id, generation, action, rationale,
+       source_ids_added, content_snapshot, created_at
+     ) VALUES (
+       ?, ?, ?, ?, ?,
+       ?, ?, ?
+     )`
+  ).run(
+    data.id,
+    data.skill_id,
+    data.generation,
+    data.action,
+    data.rationale,
+    data.source_ids_added ?? "[]",
+    data.content_snapshot,
+    data.created_at
+  );
+  return toLineageRow(
+    db.prepare(`SELECT ${SELECT_COLUMNS6} FROM skill_lineage WHERE id = ?`).get(data.id)
+  );
+}
+function listLineageForSkill(skillId, limit = 50) {
+  const db = getDatabase();
+  const rows = db.prepare(
+    `SELECT ${SELECT_COLUMNS6}
+     FROM skill_lineage
+     WHERE skill_id = ?
+     ORDER BY generation DESC
+     LIMIT ?`
+  ).all(skillId, limit);
+  return rows.map(toLineageRow);
+}
+
 // src/db/queries/batches.ts
 var DEFAULT_UNPROCESSED_LIMIT = 100;
 var BATCHES_DEFAULT_LIMIT = 200;
@@ -1020,7 +1558,7 @@ var BATCH_COLUMNS = [
   "machine_id",
   "synced_at"
 ];
-var SELECT_COLUMNS5 = BATCH_COLUMNS.join(", ");
+var SELECT_COLUMNS7 = BATCH_COLUMNS.join(", ");
 function toBatchRow(row) {
   return {
     id: row.id,
@@ -1067,7 +1605,7 @@ function getUnprocessedBatches(options = {}) {
   params.push(limit);
   const where = conditions.join(" AND ");
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS5}
+    `SELECT ${SELECT_COLUMNS7}
      FROM prompt_batches
      WHERE ${where}
      ORDER BY id ASC
@@ -1084,7 +1622,7 @@ function incrementActivityCount(id) {
   ).run(id);
   if (info.changes === 0) return null;
   return toBatchRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM prompt_batches WHERE id = ?`).get(id)
+    db.prepare(`SELECT ${SELECT_COLUMNS7} FROM prompt_batches WHERE id = ?`).get(id)
   );
 }
 function markBatchProcessed(id) {
@@ -1096,7 +1634,7 @@ function markBatchProcessed(id) {
   ).run(PROCESSED_FLAG, id);
   if (info.changes === 0) return null;
   return toBatchRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM prompt_batches WHERE id = ?`).get(id)
+    db.prepare(`SELECT ${SELECT_COLUMNS7} FROM prompt_batches WHERE id = ?`).get(id)
   );
 }
 function findBatchByPromptPrefix(sessionId, promptPrefix) {
@@ -1136,7 +1674,7 @@ function insertBatchStateless(data) {
   );
   const batchId = Number(info.lastInsertRowid);
   return toBatchRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM prompt_batches WHERE id = ?`).get(batchId)
+    db.prepare(`SELECT ${SELECT_COLUMNS7} FROM prompt_batches WHERE id = ?`).get(batchId)
   );
 }
 function closeOpenBatches(sessionId, endedAt) {
@@ -1157,7 +1695,7 @@ function setResponseSummary(batchId, summary) {
 function getLatestBatch(sessionId) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS5} FROM prompt_batches
+    `SELECT ${SELECT_COLUMNS7} FROM prompt_batches
      WHERE session_id = ?
      ORDER BY id DESC LIMIT 1`
   ).get(sessionId);
@@ -1169,7 +1707,7 @@ function listBatchesBySession(sessionId, options = {}) {
   const limit = options.limit ?? BATCHES_DEFAULT_LIMIT;
   const offset = options.offset ?? 0;
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS5}
+    `SELECT ${SELECT_COLUMNS7}
      FROM prompt_batches
      WHERE session_id = ?
      ORDER BY prompt_number ASC
@@ -1205,7 +1743,7 @@ var GRAPH_EDGE_COLUMNS = [
   "machine_id",
   "synced_at"
 ];
-var SELECT_COLUMNS6 = GRAPH_EDGE_COLUMNS.join(", ");
+var SELECT_COLUMNS8 = GRAPH_EDGE_COLUMNS.join(", ");
 function toGraphEdgeRow(row) {
   return {
     id: row.id,
@@ -1246,7 +1784,7 @@ function insertGraphEdge(data) {
     data.machine_id ?? getTeamMachineId()
   );
   const row = toGraphEdgeRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS6} FROM graph_edges WHERE id = ?`).get(id)
+    db.prepare(`SELECT ${SELECT_COLUMNS8} FROM graph_edges WHERE id = ?`).get(id)
   );
   syncRow("graph_edges", row);
   return row;
@@ -1275,7 +1813,7 @@ function listGraphEdges(options = {}) {
   const limit = options.limit ?? QUERY_DEFAULT_LIST_LIMIT;
   params.push(limit);
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS6}
+    `SELECT ${SELECT_COLUMNS8}
      FROM graph_edges
      ${where}
      ORDER BY created_at DESC
@@ -1295,7 +1833,7 @@ function getGraphForNode(nodeId, nodeType, options) {
     const frontierArray = Array.from(frontier);
     const placeholders = frontierArray.map(() => `?`).join(", ");
     const rows = db.prepare(
-      `SELECT ${SELECT_COLUMNS6}
+      `SELECT ${SELECT_COLUMNS8}
        FROM graph_edges
        WHERE source_id IN (${placeholders}) OR target_id IN (${placeholders})`
     ).all(...frontierArray, ...frontierArray);
@@ -1336,7 +1874,7 @@ var ENTITY_COLUMNS = [
   "machine_id",
   "synced_at"
 ];
-var SELECT_COLUMNS7 = ENTITY_COLUMNS.join(", ");
+var SELECT_COLUMNS9 = ENTITY_COLUMNS.join(", ");
 function toEntityRow(row) {
   return {
     id: row.id,
@@ -1370,7 +1908,7 @@ function insertEntity(data) {
     data.machine_id ?? getTeamMachineId()
   );
   const row = toEntityRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS7} FROM entities WHERE agent_id = ? AND type = ? AND name = ?`).get(
+    db.prepare(`SELECT ${SELECT_COLUMNS9} FROM entities WHERE agent_id = ? AND type = ? AND name = ?`).get(
       data.agent_id,
       data.type,
       data.name
@@ -1382,7 +1920,7 @@ function insertEntity(data) {
 function getEntity(id) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS7} FROM entities WHERE id = ?`
+    `SELECT ${SELECT_COLUMNS9} FROM entities WHERE id = ?`
   ).get(id);
   if (!row) return null;
   return toEntityRow(row);
@@ -1423,7 +1961,7 @@ function listEntities(options = {}) {
   params.push(limit);
   params.push(offset);
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS7}
+    `SELECT ${SELECT_COLUMNS9}
      FROM entities
      ${where}
      ORDER BY last_seen DESC
@@ -1433,65 +1971,6 @@ function listEntities(options = {}) {
   return rows.map(toEntityRow);
 }
 
-// src/db/queries/digest-extracts.ts
-var EXTRACT_COLUMNS = [
-  "id",
-  "agent_id",
-  "tier",
-  "content",
-  "substrate_hash",
-  "generated_at",
-  "machine_id",
-  "synced_at"
-];
-var SELECT_COLUMNS8 = EXTRACT_COLUMNS.join(", ");
-function toDigestExtractRow(row) {
-  return {
-    id: row.id,
-    agent_id: row.agent_id,
-    tier: row.tier,
-    content: row.content,
-    substrate_hash: row.substrate_hash ?? null,
-    generated_at: row.generated_at,
-    machine_id: row.machine_id ?? "local",
-    synced_at: row.synced_at ?? null
-  };
-}
-function upsertDigestExtract(data) {
-  const db = getDatabase();
-  db.prepare(
-    `INSERT INTO digest_extracts (agent_id, tier, content, generated_at)
-     VALUES (?, ?, ?, ?)
-     ON CONFLICT (agent_id, tier) DO UPDATE SET
-       content = EXCLUDED.content,
-       generated_at = EXCLUDED.generated_at`
-  ).run(data.agent_id, data.tier, data.content, data.generated_at);
-  const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS8} FROM digest_extracts WHERE agent_id = ? AND tier = ?`
-  ).get(data.agent_id, data.tier);
-  return toDigestExtractRow(row);
-}
-function getDigestExtract(agentId, tier) {
-  const db = getDatabase();
-  const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS8} FROM digest_extracts
-     WHERE agent_id = ? AND tier = ?`
-  ).get(agentId, tier);
-  if (!row) return null;
-  return toDigestExtractRow(row);
-}
-function listDigestExtracts(agentId) {
-  const db = getDatabase();
-  const tierPlaceholders = DIGEST_TIERS.map(() => "?").join(", ");
-  const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS8}
-     FROM digest_extracts
-     WHERE agent_id = ? AND tier IN (${tierPlaceholders})
-     ORDER BY tier ASC`
-  ).all(agentId, ...DIGEST_TIERS);
-  return rows.map(toDigestExtractRow);
-}
-
 // src/db/queries/lineage.ts
 function createSporeLineage(spore) {
   if (spore.session_id) {
@@ -1558,7 +2037,7 @@ var REPORT_COLUMNS = [
   "details",
   "created_at"
 ];
-var SELECT_COLUMNS9 = REPORT_COLUMNS.join(", ");
+var SELECT_COLUMNS10 = REPORT_COLUMNS.join(", ");
 function toReportRow(row) {
   return {
     id: row.id,
@@ -1588,13 +2067,13 @@ function insertReport(data) {
   );
   const reportId = Number(info.lastInsertRowid);
   return toReportRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS9} FROM agent_reports WHERE id = ?`).get(reportId)
+    db.prepare(`SELECT ${SELECT_COLUMNS10} FROM agent_reports WHERE id = ?`).get(reportId)
   );
 }
 function listReports(runId) {
   const db = getDatabase();
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS9}
+    `SELECT ${SELECT_COLUMNS10}
      FROM agent_reports
      WHERE run_id = ?
      ORDER BY created_at ASC`
@@ -1651,6 +2130,14 @@ export {
   getDigestExtract,
   listDigestExtracts,
   errorMessage,
+  setState,
+  getStatesForAgent,
+  descriptionSimilarity,
+  topicOverlapSimilarity,
+  DESCRIPTION_DUPLICATE_THRESHOLD,
+  TOPIC_OVERLAP_THRESHOLD,
+  checkFrontmatterPreservation,
+  validateSkillContent,
   SKILL_GENERATE_TASK,
   buildTaskInstruction,
   isInstructionRequiredTask,
@@ -1671,4 +2158,4 @@ export {
   hasConfiguredProvider,
   resolveRunConfig
 };
-//# sourceMappingURL=chunk-JDI4DPWD.js.map
+//# sourceMappingURL=chunk-C3EGL5JX.js.map