@goondocks/myco 0.19.0 → 0.19.2

package/dist/{chunk-RXROZBSK.js → chunk-THZKOZ4M.js}

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   loadAllTasks
-} from "./chunk-3TPD6HEF.js";
+} from "./chunk-KYH4V4ML.js";
 import {
   getAgent,
   getDefaultTask,
@@ -9,23 +9,23 @@ import {
   loadAgentDefinition,
   resolveDefinitionsDir,
   resolveEffectiveConfig
-} from "./chunk-AELJ4PS5.js";
+} from "./chunk-Q4QD6LJT.js";
 import {
   getSpore,
   listSporeIdsSince,
   listSpores
-} from "./chunk-REN37KYI.js";
+} from "./chunk-FGKCE5AE.js";
 import {
   getSession,
   listSessions
-} from "./chunk-2OO3BRFK.js";
+} from "./chunk-Q6OEZM3S.js";
 import {
   getTeamMachineId,
   syncRow
-} from "./chunk-INWD6AIQ.js";
+} from "./chunk-AULBWINA.js";
 import {
   loadConfig
-} from "./chunk-MDEUXYJG.js";
+} from "./chunk-3C4LT4BW.js";
 import {
   getDatabase
 } from "./chunk-MYX5NCRH.js";
@@ -39,7 +39,7 @@ import {
   GRAPH_EDGE_DEFAULT_CONFIDENCE,
   QUERY_DEFAULT_LIST_LIMIT,
   epochSeconds
-} from "./chunk-W4VHC2ES.js";
+} from "./chunk-I54KLC6H.js";
 
 // src/notifications/notify.ts
 import crypto from "crypto";
@@ -171,13 +171,273 @@ function errorMessage(err) {
   }
 }
 
+// src/db/queries/runs.ts
+var DEFAULT_LIST_LIMIT2 = 100;
+var DEFAULT_STATUS = "pending";
+var STATUS_RUNNING = "running";
+var STATUS_COMPLETED = "completed";
+var STATUS_FAILED = "failed";
+var RUN_COLUMNS = [
+  "id",
+  "agent_id",
+  "task",
+  "instruction",
+  "status",
+  "started_at",
+  "completed_at",
+  "tokens_used",
+  "cost_usd",
+  "actions_taken",
+  "error"
+];
+var SELECT_COLUMNS = RUN_COLUMNS.join(", ");
+function toRunRow(row) {
+  return {
+    id: row.id,
+    agent_id: row.agent_id,
+    task: row.task ?? null,
+    instruction: row.instruction ?? null,
+    status: row.status,
+    started_at: row.started_at ?? null,
+    completed_at: row.completed_at ?? null,
+    tokens_used: row.tokens_used ?? null,
+    cost_usd: row.cost_usd ?? null,
+    actions_taken: row.actions_taken ?? null,
+    error: row.error ?? null
+  };
+}
+function insertRun(data) {
+  const db = getDatabase();
+  db.prepare(
+    `INSERT INTO agent_runs (
+       id, agent_id, task, instruction, status,
+       started_at, completed_at, tokens_used, cost_usd,
+       actions_taken, error
+     ) VALUES (
+       ?, ?, ?, ?, ?,
+       ?, ?, ?, ?,
+       ?, ?
+     )`
+  ).run(
+    data.id,
+    data.agent_id,
+    data.task ?? null,
+    data.instruction ?? null,
+    data.status ?? DEFAULT_STATUS,
+    data.started_at ?? null,
+    data.completed_at ?? null,
+    data.tokens_used ?? null,
+    data.cost_usd ?? null,
+    data.actions_taken ?? null,
+    data.error ?? null
+  );
+  return toRunRow(
+    db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`).get(data.id)
+  );
+}
+function getRun(id) {
+  const db = getDatabase();
+  const row = db.prepare(
+    `SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`
+  ).get(id);
+  if (!row) return null;
+  return toRunRow(row);
+}
+function buildRunsWhere(options) {
+  const conditions = [];
+  const params = [];
+  if (options.agent_id !== void 0) {
+    conditions.push(`agent_id = ?`);
+    params.push(options.agent_id);
+  }
+  if (options.status !== void 0) {
+    conditions.push(`status = ?`);
+    params.push(options.status);
+  }
+  if (options.task !== void 0) {
+    conditions.push(`task = ?`);
+    params.push(options.task);
+  }
+  if (options.search !== void 0 && options.search.length > 0) {
+    conditions.push(`task LIKE ?`);
+    params.push(`%${options.search}%`);
+  }
+  return {
+    where: conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "",
+    params
+  };
+}
+function listRuns(options = {}) {
+  const db = getDatabase();
+  const { where, params } = buildRunsWhere(options);
+  const limit = options.limit ?? DEFAULT_LIST_LIMIT2;
+  const offset = options.offset ?? 0;
+  const rows = db.prepare(
+    `SELECT ${SELECT_COLUMNS}
+     FROM agent_runs
+     ${where}
+     ORDER BY started_at DESC NULLS LAST
+     LIMIT ?
+     OFFSET ?`
+  ).all(...params, limit, offset);
+  return rows.map(toRunRow);
+}
+function countRuns(options = {}) {
+  const db = getDatabase();
+  const { where, params } = buildRunsWhere(options);
+  const row = db.prepare(
+    `SELECT COUNT(*) as count FROM agent_runs ${where}`
+  ).get(...params);
+  return row.count;
+}
+function updateRunStatus(id, status, completion) {
+  const db = getDatabase();
+  const setClauses = ["status = ?"];
+  const params = [status];
+  if (completion?.completed_at !== void 0) {
+    setClauses.push(`completed_at = ?`);
+    params.push(completion.completed_at);
+  }
+  if (completion?.tokens_used !== void 0) {
+    setClauses.push(`tokens_used = ?`);
+    params.push(completion.tokens_used);
+  }
+  if (completion?.cost_usd !== void 0) {
+    setClauses.push(`cost_usd = ?`);
+    params.push(completion.cost_usd);
+  }
+  if (completion?.actions_taken !== void 0) {
+    setClauses.push(`actions_taken = ?`);
+    params.push(completion.actions_taken);
+  }
+  if (completion?.error !== void 0) {
+    setClauses.push(`error = ?`);
+    params.push(completion.error);
+  }
+  params.push(id);
+  const info = db.prepare(
+    `UPDATE agent_runs
+     SET ${setClauses.join(", ")}
+     WHERE id = ?`
+  ).run(...params);
+  if (info.changes === 0) return null;
+  return toRunRow(
+    db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`).get(id)
+  );
+}
+function getRunningRunForTask(agentId, taskName) {
+  const db = getDatabase();
+  const row = db.prepare(
+    `SELECT id FROM agent_runs
+     WHERE agent_id = ? AND task = ? AND status = ?
+     LIMIT 1`
+  ).get(agentId, taskName, STATUS_RUNNING);
+  return row?.id ?? null;
+}
+function getLatestRunId(agentId, taskName) {
+  const db = getDatabase();
+  if (taskName) {
+    const row2 = db.prepare(
+      `SELECT id FROM agent_runs
+       WHERE agent_id = ? AND task = ?
+       ORDER BY started_at DESC
+       LIMIT 1`
+    ).get(agentId, taskName);
+    return row2?.id ?? null;
+  }
+  const row = db.prepare(
+    `SELECT id FROM agent_runs
+     WHERE agent_id = ?
+     ORDER BY started_at DESC
+     LIMIT 1`
+  ).get(agentId);
+  return row?.id ?? null;
+}
+
+// src/agent/config-resolver.ts
+function hasConfiguredProvider(mycoConfig, taskName) {
+  const taskProvider = taskName ? mycoConfig.agent.tasks?.[taskName]?.provider : void 0;
+  return !!(taskProvider ?? mycoConfig.agent.provider);
+}
+function toProviderConfig(p) {
+  return {
+    type: p.type,
+    baseUrl: p.base_url,
+    model: p.model,
+    contextLength: p.context_length
+  };
+}
+function resolveRunConfig(agentId, requestedTask, vaultDir) {
+  const definitionsDir = resolveDefinitionsDir();
+  const definition = loadAgentDefinition(definitionsDir);
+  const agentRow = getAgent(agentId);
+  const taskRow = requestedTask ? getTask(requestedTask) : getDefaultTask(agentId);
+  const allTasks = loadAllTasks(definitionsDir, vaultDir);
+  const taskName = taskRow?.id ?? requestedTask;
+  const yamlTask = taskName ? allTasks.get(taskName) : void 0;
+  const taskOverrides = taskRow ? {
+    name: taskRow.id,
+    displayName: taskRow.display_name ?? taskRow.id,
+    description: taskRow.description ?? "",
+    agent: taskRow.agent_id,
+    prompt: taskRow.prompt,
+    isDefault: taskRow.is_default === 1,
+    ...taskRow.tool_overrides ? { toolOverrides: JSON.parse(taskRow.tool_overrides) } : {},
+    // Scalar config from YAML (model, turns, timeout) — DB doesn't store these
+    ...yamlTask?.model ? { model: yamlTask.model } : {},
+    ...yamlTask?.maxTurns ? { maxTurns: yamlTask.maxTurns } : {},
+    ...yamlTask?.timeoutSeconds ? { timeoutSeconds: yamlTask.timeoutSeconds } : {},
+    // Structural config from YAML
+    ...yamlTask?.phases ? { phases: yamlTask.phases } : {},
+    ...yamlTask?.execution ? { execution: yamlTask.execution } : {},
+    ...yamlTask?.contextQueries ? { contextQueries: yamlTask.contextQueries } : {},
+    ...yamlTask?.orchestrator ? { orchestrator: yamlTask.orchestrator } : {}
+  } : void 0;
+  const config = resolveEffectiveConfig(definition, agentRow, taskOverrides);
+  let taskProviderOverride;
+  let phaseProviderOverrides = {};
+  let taskParams;
+  try {
+    const mycoConfig = loadConfig(vaultDir);
+    const taskConfig = taskName ? mycoConfig.agent.tasks?.[taskName] : void 0;
+    const globalProvider = mycoConfig.agent.provider;
+    if (taskConfig?.provider) {
+      taskProviderOverride = toProviderConfig(taskConfig.provider);
+    } else if (globalProvider) {
+      taskProviderOverride = toProviderConfig(globalProvider);
+    }
+    if (taskConfig?.phases) {
+      for (const [phaseName, phaseConfig] of Object.entries(taskConfig.phases)) {
+        phaseProviderOverrides[phaseName] = {
+          ...phaseConfig.provider ? { provider: toProviderConfig(phaseConfig.provider) } : {},
+          ...phaseConfig.maxTurns != null ? { maxTurns: phaseConfig.maxTurns } : {}
+        };
+      }
+    }
+    const yamlParams = yamlTask?.params;
+    const configParams = taskConfig?.params;
+    if (yamlParams || configParams) {
+      taskParams = { ...yamlParams, ...configParams };
+    }
+  } catch {
+  }
+  return {
+    config,
+    definitionsDir,
+    taskProviderOverride,
+    phaseProviderOverrides,
+    taskName,
+    taskParams
+  };
+}
+
 // 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";
+var DEFAULT_STATUS2 = "identified";
 var CANDIDATE_COLUMNS = [
   "id",
   "agent_id",
@@ -194,7 +454,7 @@ var CANDIDATE_COLUMNS = [
   "updated_at",
   "synced_at"
 ];
-var SELECT_COLUMNS = CANDIDATE_COLUMNS.join(", ");
+var SELECT_COLUMNS2 = CANDIDATE_COLUMNS.join(", ");
 function toCandidateRow(row) {
   return {
     id: row.id,
@@ -252,7 +512,7 @@ function insertCandidate(data) {
     data.topic,
     data.rationale,
     data.confidence ?? DEFAULT_CONFIDENCE,
-    data.status ?? DEFAULT_STATUS,
+    data.status ?? DEFAULT_STATUS2,
     data.source_ids ?? "[]",
     data.skill_id ?? null,
     data.supersedes ?? null,
@@ -260,7 +520,7 @@ function insertCandidate(data) {
     data.created_at,
     data.updated_at
   );
-  const raw = db.prepare(`SELECT ${SELECT_COLUMNS} FROM skill_candidates WHERE id = ?`).get(data.id);
+  const raw = db.prepare(`SELECT ${SELECT_COLUMNS2} FROM skill_candidates WHERE id = ?`).get(data.id);
   if (!raw) throw new Error(`Failed to insert skill candidate: ${data.id}`);
   const row = toCandidateRow(raw);
   syncRow("skill_candidates", row);
@@ -269,7 +529,7 @@ function insertCandidate(data) {
 function getCandidate(id) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS} FROM skill_candidates WHERE id = ?`
+    `SELECT ${SELECT_COLUMNS2} FROM skill_candidates WHERE id = ?`
   ).get(id);
   if (!row) return null;
   return toCandidateRow(row);
@@ -280,7 +540,7 @@ function listCandidates(options = {}) {
   const limit = options.limit ?? DEFAULT_LIST_LIMIT;
   const offset = options.offset ?? 0;
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS}
+    `SELECT ${SELECT_COLUMNS2}
      FROM skill_candidates
      ${where}
      ORDER BY confidence DESC, created_at DESC
@@ -338,7 +598,7 @@ function listCandidatesWithCount(options = {}) {
   const limit = options.limit ?? DEFAULT_LIST_LIMIT;
   const offset = options.offset ?? 0;
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS}, COUNT(*) OVER () AS __total
+    `SELECT ${SELECT_COLUMNS2}, COUNT(*) OVER () AS __total
      FROM skill_candidates
      ${where}
      ORDER BY confidence DESC, created_at DESC
@@ -370,7 +630,7 @@ function deleteCandidate(id) {
 }
 
 // src/db/queries/skill-records.ts
-var DEFAULT_STATUS2 = "active";
+var DEFAULT_STATUS3 = "active";
 var DEFAULT_GENERATION = 1;
 var RECORD_COLUMNS = [
   "id",
@@ -391,7 +651,7 @@ var RECORD_COLUMNS = [
   "properties",
   "synced_at"
 ];
-var SELECT_COLUMNS2 = RECORD_COLUMNS.join(", ");
+var SELECT_COLUMNS3 = RECORD_COLUMNS.join(", ");
 function toSkillRecordRow(row) {
   return {
     id: row.id,
@@ -448,7 +708,7 @@ function insertSkillRecord(data) {
     data.name,
     data.display_name,
     data.description,
-    data.status ?? DEFAULT_STATUS2,
+    data.status ?? DEFAULT_STATUS3,
     data.generation ?? DEFAULT_GENERATION,
     data.candidate_id ?? null,
     data.source_ids ?? "[]",
@@ -457,7 +717,7 @@ function insertSkillRecord(data) {
     data.updated_at,
     data.properties ?? "{}"
   );
-  const raw = db.prepare(`SELECT ${SELECT_COLUMNS2} FROM skill_records WHERE id = ?`).get(data.id);
+  const raw = db.prepare(`SELECT ${SELECT_COLUMNS3} FROM skill_records WHERE id = ?`).get(data.id);
   if (!raw) throw new Error(`Failed to insert skill record: ${data.id}`);
   const row = toSkillRecordRow(raw);
   syncRow("skill_records", row);
@@ -466,7 +726,7 @@ function insertSkillRecord(data) {
 function getSkillRecord(id) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS2} FROM skill_records WHERE id = ?`
+    `SELECT ${SELECT_COLUMNS3} FROM skill_records WHERE id = ?`
   ).get(id);
   if (!row) return null;
   return toSkillRecordRow(row);
@@ -474,7 +734,7 @@ function getSkillRecord(id) {
 function getSkillRecordByName(name) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS2} FROM skill_records WHERE name = ?`
+    `SELECT ${SELECT_COLUMNS3} FROM skill_records WHERE name = ?`
   ).get(name);
   if (!row) return null;
   return toSkillRecordRow(row);
@@ -485,7 +745,7 @@ function listSkillRecords(options = {}) {
   const limit = options.limit ?? DEFAULT_LIST_LIMIT;
   const offset = options.offset ?? 0;
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS2}
+    `SELECT ${SELECT_COLUMNS3}
      FROM skill_records
      ${where}
      ORDER BY updated_at DESC
@@ -577,7 +837,7 @@ var EXTRACT_COLUMNS = [
   "machine_id",
   "synced_at"
 ];
-var SELECT_COLUMNS3 = EXTRACT_COLUMNS.join(", ");
+var SELECT_COLUMNS4 = EXTRACT_COLUMNS.join(", ");
 function toDigestExtractRow(row) {
   return {
     id: row.id,
@@ -600,14 +860,14 @@ function upsertDigestExtract(data) {
        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 = ?`
+    `SELECT ${SELECT_COLUMNS4} 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_COLUMNS3} FROM digest_extracts
+    `SELECT ${SELECT_COLUMNS4} FROM digest_extracts
      WHERE agent_id = ? AND tier = ?`
   ).get(agentId, tier);
   if (!row) return null;
@@ -617,7 +877,7 @@ function listDigestExtracts(agentId) {
   const db = getDatabase();
   const tierPlaceholders = DIGEST_TIERS.map(() => "?").join(", ");
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS3}
+    `SELECT ${SELECT_COLUMNS4}
      FROM digest_extracts
      WHERE agent_id = ? AND tier IN (${tierPlaceholders})
      ORDER BY tier ASC`
@@ -632,7 +892,7 @@ var STATE_COLUMNS = [
   "value",
   "updated_at"
 ];
-var SELECT_COLUMNS4 = STATE_COLUMNS.join(", ");
+var SELECT_COLUMNS5 = STATE_COLUMNS.join(", ");
 function toAgentStateRow(row) {
   return {
     agent_id: row.agent_id,
@@ -644,7 +904,7 @@ function toAgentStateRow(row) {
 function getState(agentId, key) {
   const db = getDatabase();
   const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS4} FROM agent_state WHERE agent_id = ? AND key = ?`
+    `SELECT ${SELECT_COLUMNS5} FROM agent_state WHERE agent_id = ? AND key = ?`
   ).get(agentId, key);
   if (!row) return null;
   return toAgentStateRow(row);
@@ -659,13 +919,13 @@ function setState(agentId, key, value, updatedAt) {
        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)
+    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM agent_state WHERE agent_id = ? AND key = ?`).get(agentId, key)
   );
 }
 function getStatesForAgent(agentId) {
   const db = getDatabase();
   const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS4}
+    `SELECT ${SELECT_COLUMNS5}
      FROM agent_state
      WHERE agent_id = ?
      ORDER BY key ASC`
@@ -981,6 +1241,7 @@ function buildSkillSurveyInstruction(agentId) {
   const wisdomSpores = listSpores({
     observation_type: "wisdom",
     limit: SURVEY_MAX_WISDOM_SPORES,
+    includeActive: false,
     ...sinceFilter
   });
   if (wisdomSpores.length > 0) {
@@ -993,11 +1254,13 @@ function buildSkillSurveyInstruction(agentId) {
   const decisions = listSpores({
     observation_type: "decision",
     limit: 20,
+    includeActive: false,
     ...sinceFilter
   });
   const gotchas = listSpores({
     observation_type: "gotcha",
     limit: 10,
+    includeActive: false,
     ...sinceFilter
   });
   if (decisions.length > 0 || gotchas.length > 0) {
@@ -1009,6 +1272,7 @@ function buildSkillSurveyInstruction(agentId) {
   }
   const sessions = listSessions({
     limit: SURVEY_MAX_SESSIONS,
+    includeActive: false,
     ...sinceFilter
   });
   if (sessions.length > 0) {
@@ -1100,376 +1364,116 @@ function buildSkillEvolveInstruction(params, projectRoot, similarityProvider) {
     }
     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}`,
-    `max_skills_per_run: ${maxSkillsPerRun}`
-  ];
-  for (const skill of needsAssessment) {
-    parts.push("");
-    parts.push("---");
-    parts.push(`## Skill: ${skill.name} (gen ${skill.generation})`);
-    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: ${s.headings.join(" | ")}`);
-    }
-  }
-  const narrowSkills = structures.filter((s) => s.narrow);
-  if (narrowSkills.length > 0) {
-    parts.push("");
-    parts.push("## Mechanically Narrow Skills (<2 H2 sections)");
-    parts.push("These skills have insufficient section breadth for domain-level standalone status.");
-    parts.push("Determine which broader skill each should be absorbed into.");
-    for (const s of narrowSkills) {
-      parts.push(`- **${s.name}**: ${s.sectionCount} section(s). Headings: ${s.headings.length > 0 ? s.headings.join(" | ") : "(none)"}`);
-    }
-  }
-  if (overlaps.length > 0) {
-    parts.push("");
-    parts.push("## Pre-computed Token Overlap");
-    parts.push("Pairs flagged by description token similarity AND/OR heading overlap:");
-    for (const o of overlaps) {
-      parts.push(`- **${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, 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, projectRoot, similarityProvider);
-      return instruction ? { instruction } : void 0;
-    }
-    default:
-      return void 0;
-  }
-}
-function isInstructionRequiredTask(taskName) {
-  return taskName === SKILL_GENERATE_TASK || taskName === SKILL_EVOLVE_TASK || taskName === SKILL_SURVEY_TASK;
-}
-
-// src/db/queries/runs.ts
-var DEFAULT_LIST_LIMIT2 = 100;
-var DEFAULT_STATUS3 = "pending";
-var STATUS_RUNNING = "running";
-var STATUS_COMPLETED = "completed";
-var STATUS_FAILED = "failed";
-var RUN_COLUMNS = [
-  "id",
-  "agent_id",
-  "task",
-  "instruction",
-  "status",
-  "started_at",
-  "completed_at",
-  "tokens_used",
-  "cost_usd",
-  "actions_taken",
-  "error"
-];
-var SELECT_COLUMNS5 = RUN_COLUMNS.join(", ");
-function toRunRow(row) {
-  return {
-    id: row.id,
-    agent_id: row.agent_id,
-    task: row.task ?? null,
-    instruction: row.instruction ?? null,
-    status: row.status,
-    started_at: row.started_at ?? null,
-    completed_at: row.completed_at ?? null,
-    tokens_used: row.tokens_used ?? null,
-    cost_usd: row.cost_usd ?? null,
-    actions_taken: row.actions_taken ?? null,
-    error: row.error ?? null
-  };
-}
-function insertRun(data) {
-  const db = getDatabase();
-  db.prepare(
-    `INSERT INTO agent_runs (
-       id, agent_id, task, instruction, status,
-       started_at, completed_at, tokens_used, cost_usd,
-       actions_taken, error
-     ) VALUES (
-       ?, ?, ?, ?, ?,
-       ?, ?, ?, ?,
-       ?, ?
-     )`
-  ).run(
-    data.id,
-    data.agent_id,
-    data.task ?? null,
-    data.instruction ?? null,
-    data.status ?? DEFAULT_STATUS3,
-    data.started_at ?? null,
-    data.completed_at ?? null,
-    data.tokens_used ?? null,
-    data.cost_usd ?? null,
-    data.actions_taken ?? null,
-    data.error ?? null
-  );
-  return toRunRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`).get(data.id)
-  );
-}
-function getRun(id) {
-  const db = getDatabase();
-  const row = db.prepare(
-    `SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`
-  ).get(id);
-  if (!row) return null;
-  return toRunRow(row);
-}
-function buildRunsWhere(options) {
-  const conditions = [];
-  const params = [];
-  if (options.agent_id !== void 0) {
-    conditions.push(`agent_id = ?`);
-    params.push(options.agent_id);
-  }
-  if (options.status !== void 0) {
-    conditions.push(`status = ?`);
-    params.push(options.status);
-  }
-  if (options.task !== void 0) {
-    conditions.push(`task = ?`);
-    params.push(options.task);
-  }
-  if (options.search !== void 0 && options.search.length > 0) {
-    conditions.push(`task LIKE ?`);
-    params.push(`%${options.search}%`);
-  }
-  return {
-    where: conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "",
-    params
-  };
-}
-function listRuns(options = {}) {
-  const db = getDatabase();
-  const { where, params } = buildRunsWhere(options);
-  const limit = options.limit ?? DEFAULT_LIST_LIMIT2;
-  const offset = options.offset ?? 0;
-  const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS5}
-     FROM agent_runs
-     ${where}
-     ORDER BY started_at DESC NULLS LAST
-     LIMIT ?
-     OFFSET ?`
-  ).all(...params, limit, offset);
-  return rows.map(toRunRow);
-}
-function countRuns(options = {}) {
-  const db = getDatabase();
-  const { where, params } = buildRunsWhere(options);
-  const row = db.prepare(
-    `SELECT COUNT(*) as count FROM agent_runs ${where}`
-  ).get(...params);
-  return row.count;
-}
-function updateRunStatus(id, status, completion) {
-  const db = getDatabase();
-  const setClauses = ["status = ?"];
-  const params = [status];
-  if (completion?.completed_at !== void 0) {
-    setClauses.push(`completed_at = ?`);
-    params.push(completion.completed_at);
-  }
-  if (completion?.tokens_used !== void 0) {
-    setClauses.push(`tokens_used = ?`);
-    params.push(completion.tokens_used);
+    structures.push({
+      name: skill.name,
+      sectionCount: headings.length,
+      headings,
+      narrow: headings.length < MIN_SECTIONS_FOR_STANDALONE
+    });
   }
-  if (completion?.cost_usd !== void 0) {
-    setClauses.push(`cost_usd = ?`);
-    params.push(completion.cost_usd);
+  const overlaps = [];
+  for (let i = 0; i < allSkills.length; i++) {
+    for (let j = i + 1; j < allSkills.length; j++) {
+      const a = allSkills[i];
+      const b = allSkills[j];
+      const descJaccard = descriptionSimilarity(a.description, b.description);
+      const aHeadings = skillHeadings.get(a.name) ?? [];
+      const bHeadings = skillHeadings.get(b.name) ?? [];
+      const ho = headingOverlap(aHeadings, bHeadings);
+      const descFlag = descJaccard >= DESCRIPTION_DUPLICATE_THRESHOLD * 0.75;
+      const headingFlag = ho.score >= 0.4;
+      if (!descFlag && !headingFlag) continue;
+      const verdict = descJaccard >= DESCRIPTION_DUPLICATE_THRESHOLD || ho.score >= 0.5 ? "potential-merge" : "potential-narrow";
+      overlaps.push({
+        skillA: a.name,
+        skillB: b.name,
+        descriptionJaccard: Math.round(descJaccard * 100) / 100,
+        headingOverlap: Math.round(ho.score * 100) / 100,
+        sharedHeadings: ho.shared,
+        verdict
+      });
+    }
   }
-  if (completion?.actions_taken !== void 0) {
-    setClauses.push(`actions_taken = ?`);
-    params.push(completion.actions_taken);
+  const parts = [
+    `${needsAssessment.length} skill(s) need assessment.`,
+    `assess_interval_hours: ${assessIntervalHours}`,
+    `max_skills_per_run: ${maxSkillsPerRun}`
+  ];
+  for (const skill of needsAssessment) {
+    parts.push("");
+    parts.push("---");
+    parts.push(`## Skill: ${skill.name} (gen ${skill.generation})`);
+    parts.push(`id: ${skill.id}`);
+    parts.push(`description: ${skill.description}`);
+    parts.push(`new_spore_ids: ${JSON.stringify(skill.newSporeIds)}`);
   }
-  if (completion?.error !== void 0) {
-    setClauses.push(`error = ?`);
-    params.push(completion.error);
+  parts.push("");
+  parts.push("## All Active Skills (for inventory analysis)");
+  for (const s of structures) {
+    const skill = allSkills.find((sk) => sk.name === s.name);
+    const narrowTag = s.narrow ? " **[NARROW \u2014 <2 sections]**" : "";
+    parts.push(`- **${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(" | ")}`);
+    }
   }
-  params.push(id);
-  const info = db.prepare(
-    `UPDATE agent_runs
-     SET ${setClauses.join(", ")}
-     WHERE id = ?`
-  ).run(...params);
-  if (info.changes === 0) return null;
-  return toRunRow(
-    db.prepare(`SELECT ${SELECT_COLUMNS5} FROM agent_runs WHERE id = ?`).get(id)
-  );
-}
-function getRunningRunForTask(agentId, taskName) {
-  const db = getDatabase();
-  const row = db.prepare(
-    `SELECT id FROM agent_runs
-     WHERE agent_id = ? AND task = ? AND status = ?
-     LIMIT 1`
-  ).get(agentId, taskName, STATUS_RUNNING);
-  return row?.id ?? null;
-}
-function getLatestRunId(agentId, taskName) {
-  const db = getDatabase();
-  if (taskName) {
-    const row2 = db.prepare(
-      `SELECT id FROM agent_runs
-       WHERE agent_id = ? AND task = ?
-       ORDER BY started_at DESC
-       LIMIT 1`
-    ).get(agentId, taskName);
-    return row2?.id ?? null;
+  const narrowSkills = structures.filter((s) => s.narrow);
+  if (narrowSkills.length > 0) {
+    parts.push("");
+    parts.push("## Mechanically Narrow Skills (<2 H2 sections)");
+    parts.push("These skills have insufficient section breadth for domain-level standalone status.");
+    parts.push("Determine which broader skill each should be absorbed into.");
+    for (const s of narrowSkills) {
+      parts.push(`- **${s.name}**: ${s.sectionCount} section(s). Headings: ${s.headings.length > 0 ? s.headings.join(" | ") : "(none)"}`);
+    }
   }
-  const row = db.prepare(
-    `SELECT id FROM agent_runs
-     WHERE agent_id = ?
-     ORDER BY started_at DESC
-     LIMIT 1`
-  ).get(agentId);
-  return row?.id ?? null;
-}
-
-// src/agent/config-resolver.ts
-function hasConfiguredProvider(mycoConfig, taskName) {
-  const taskProvider = taskName ? mycoConfig.agent.tasks?.[taskName]?.provider : void 0;
-  return !!(taskProvider ?? mycoConfig.agent.provider);
-}
-function toProviderConfig(p) {
-  return {
-    type: p.type,
-    baseUrl: p.base_url,
-    model: p.model,
-    contextLength: p.context_length
-  };
-}
-function resolveRunConfig(agentId, requestedTask, vaultDir) {
-  const definitionsDir = resolveDefinitionsDir();
-  const definition = loadAgentDefinition(definitionsDir);
-  const agentRow = getAgent(agentId);
-  const taskRow = requestedTask ? getTask(requestedTask) : getDefaultTask(agentId);
-  const allTasks = loadAllTasks(definitionsDir, vaultDir);
-  const taskName = taskRow?.id ?? requestedTask;
-  const yamlTask = taskName ? allTasks.get(taskName) : void 0;
-  const taskOverrides = taskRow ? {
-    name: taskRow.id,
-    displayName: taskRow.display_name ?? taskRow.id,
-    description: taskRow.description ?? "",
-    agent: taskRow.agent_id,
-    prompt: taskRow.prompt,
-    isDefault: taskRow.is_default === 1,
-    ...taskRow.tool_overrides ? { toolOverrides: JSON.parse(taskRow.tool_overrides) } : {},
-    // Scalar config from YAML (model, turns, timeout) — DB doesn't store these
-    ...yamlTask?.model ? { model: yamlTask.model } : {},
-    ...yamlTask?.maxTurns ? { maxTurns: yamlTask.maxTurns } : {},
-    ...yamlTask?.timeoutSeconds ? { timeoutSeconds: yamlTask.timeoutSeconds } : {},
-    // Structural config from YAML
-    ...yamlTask?.phases ? { phases: yamlTask.phases } : {},
-    ...yamlTask?.execution ? { execution: yamlTask.execution } : {},
-    ...yamlTask?.contextQueries ? { contextQueries: yamlTask.contextQueries } : {},
-    ...yamlTask?.orchestrator ? { orchestrator: yamlTask.orchestrator } : {}
-  } : void 0;
-  const config = resolveEffectiveConfig(definition, agentRow, taskOverrides);
-  let taskProviderOverride;
-  let phaseProviderOverrides = {};
-  let taskParams;
-  try {
-    const mycoConfig = loadConfig(vaultDir);
-    const taskConfig = taskName ? mycoConfig.agent.tasks?.[taskName] : void 0;
-    const globalProvider = mycoConfig.agent.provider;
-    if (taskConfig?.provider) {
-      taskProviderOverride = toProviderConfig(taskConfig.provider);
-    } else if (globalProvider) {
-      taskProviderOverride = toProviderConfig(globalProvider);
+  if (overlaps.length > 0) {
+    parts.push("");
+    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: ${o.sharedHeadings.join("; ")}`);
+      }
     }
-    if (taskConfig?.phases) {
-      for (const [phaseName, phaseConfig] of Object.entries(taskConfig.phases)) {
-        phaseProviderOverrides[phaseName] = {
-          ...phaseConfig.provider ? { provider: toProviderConfig(phaseConfig.provider) } : {},
-          ...phaseConfig.maxTurns != null ? { maxTurns: phaseConfig.maxTurns } : {}
-        };
+  }
+  if (similarityProvider) {
+    const idToName = new Map(allSkills.map((s) => [s.id, s.name]));
+    try {
+      const semanticPairs = similarityProvider.pairwiseSimilarity("skill_records", 0.65);
+      if (semanticPairs.length > 0) {
+        parts.push("");
+        parts.push("## Semantic Similarity (embedding cosine distance)");
+        parts.push("Pairs with cosine similarity >= 0.65. This is the STRONGEST overlap signal.");
+        parts.push("High similarity (>0.8) means the skills describe nearly identical procedures.");
+        for (const p of semanticPairs) {
+          const nameA = idToName.get(p.idA) ?? p.idA;
+          const nameB = idToName.get(p.idB) ?? p.idB;
+          parts.push(`- **${nameA}** <-> **${nameB}**: cosine=${p.similarity}`);
+        }
       }
+    } catch {
     }
-    const yamlParams = yamlTask?.params;
-    const configParams = taskConfig?.params;
-    if (yamlParams || configParams) {
-      taskParams = { ...yamlParams, ...configParams };
+  }
+  return parts.join("\n");
+}
+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, projectRoot, similarityProvider);
+      return instruction ? { instruction } : void 0;
     }
-  } catch {
+    default:
+      return void 0;
   }
-  return {
-    config,
-    definitionsDir,
-    taskProviderOverride,
-    phaseProviderOverrides,
-    taskName,
-    taskParams
-  };
+}
+function isInstructionRequiredTask(taskName) {
+  return taskName === SKILL_GENERATE_TASK || taskName === SKILL_EVOLVE_TASK || taskName === SKILL_SURVEY_TASK;
 }
 
 // src/db/queries/skill-lineage.ts
@@ -1601,6 +1605,11 @@ function getUnprocessedBatches(options = {}) {
     conditions.push(`id > ?`);
     params.push(options.after_id);
   }
+  if (options.includeActive === false) {
+    conditions.push(
+      `EXISTS (SELECT 1 FROM sessions s WHERE s.id = prompt_batches.session_id AND s.status != 'active')`
+    );
+  }
   const limit = options.limit ?? DEFAULT_UNPROCESSED_LIMIT;
   params.push(limit);
   const where = conditions.join(" AND ");
@@ -2120,42 +2129,42 @@ export {
   getLatestBatch,
   listBatchesBySession,
   countBatchesBySession,
+  errorMessage,
+  STATUS_RUNNING,
+  STATUS_COMPLETED,
+  STATUS_FAILED,
+  insertRun,
+  getRun,
+  listRuns,
+  countRuns,
+  updateRunStatus,
+  getRunningRunForTask,
+  getLatestRunId,
+  setState,
+  getStatesForAgent,
   insertGraphEdge,
   listGraphEdges,
   getGraphForNode,
   insertEntity,
   getEntity,
   listEntities,
+  createSporeLineage,
+  createBatchLineage,
   upsertDigestExtract,
   getDigestExtract,
   listDigestExtracts,
-  errorMessage,
-  setState,
-  getStatesForAgent,
+  insertReport,
+  listReports,
   descriptionSimilarity,
   topicOverlapSimilarity,
   DESCRIPTION_DUPLICATE_THRESHOLD,
   TOPIC_OVERLAP_THRESHOLD,
   checkFrontmatterPreservation,
   validateSkillContent,
+  hasConfiguredProvider,
+  resolveRunConfig,
   SKILL_GENERATE_TASK,
   buildTaskInstruction,
-  isInstructionRequiredTask,
-  STATUS_RUNNING,
-  STATUS_COMPLETED,
-  STATUS_FAILED,
-  insertRun,
-  getRun,
-  listRuns,
-  countRuns,
-  updateRunStatus,
-  getRunningRunForTask,
-  getLatestRunId,
-  createSporeLineage,
-  createBatchLineage,
-  insertReport,
-  listReports,
-  hasConfiguredProvider,
-  resolveRunConfig
+  isInstructionRequiredTask
 };
-//# sourceMappingURL=chunk-RXROZBSK.js.map
+//# sourceMappingURL=chunk-THZKOZ4M.js.map