@goondocks/myco 0.18.0 → 0.19.0

package/dist/{executor-NSPRTH4M.js → executor-ICTRRUBY.js}

@@ -1,17 +1,22 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
+  DESCRIPTION_DUPLICATE_THRESHOLD,
   SKILL_GENERATE_TASK,
   STATUS_COMPLETED,
   STATUS_FAILED,
   STATUS_RUNNING,
+  TOPIC_OVERLAP_THRESHOLD,
+  checkFrontmatterPreservation,
   createSporeLineage,
   deleteCandidate,
   deleteSkillRecordCascade,
+  descriptionSimilarity,
   errorMessage,
   getCandidate,
   getRunningRunForTask,
   getSkillRecord,
   getSkillRecordByName,
+  getStatesForAgent,
   getUnprocessedBatches,
   insertCandidate,
   insertEntity,
@@ -28,25 +33,28 @@ import {
   markBatchProcessed,
   notify,
   resolveRunConfig,
+  setState,
+  topicOverlapSimilarity,
   updateCandidate,
   updateRunStatus,
   updateSkillRecord,
-  upsertDigestExtract
-} from "./chunk-JDI4DPWD.js";
+  upsertDigestExtract,
+  validateSkillContent
+} from "./chunk-RXROZBSK.js";
 import {
   fullTextSearch
-} from "./chunk-NZI7WBZI.js";
-import "./chunk-RAV5YMRU.js";
+} from "./chunk-2DF4OZ2D.js";
+import "./chunk-3TPD6HEF.js";
 import {
   getDefaultTask,
   loadSystemPrompt
-} from "./chunk-NI23QCHB.js";
+} from "./chunk-AELJ4PS5.js";
 import {
   insertTurn
 } from "./chunk-QLCD77AN.js";
 import {
   insertResolutionEvent
-} from "./chunk-U3J2DDSR.js";
+} from "./chunk-SCI55NKY.js";
 import {
   cleanupStagedSkill,
   readStagedManifest,
@@ -54,24 +62,24 @@ import {
   writeStagedManifest,
   writeStagedSkill
 } from "./chunk-U5EW2VIQ.js";
-import "./chunk-IB76KGBY.js";
+import "./chunk-POEPHBQK.js";
 import {
   DEFAULT_IMPORTANCE,
   insertSpore,
   listSpores,
   updateSporeStatus
-} from "./chunk-7OYXB2NM.js";
+} from "./chunk-REN37KYI.js";
 import {
   listSessions,
   updateSession
-} from "./chunk-U7GJTVSX.js";
-import "./chunk-O3TRN3RC.js";
+} from "./chunk-2OO3BRFK.js";
+import "./chunk-INWD6AIQ.js";
 import {
   AGENT_SETTABLE_STATUSES,
   CANDIDATE_STATUS,
   createSchema
-} from "./chunk-OW433Q4C.js";
-import "./chunk-2V7HR7HB.js";
+} from "./chunk-2LN2BBKA.js";
+import "./chunk-MDEUXYJG.js";
 import {
   getDatabase,
   initDatabase,
@@ -79,7 +87,7 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   getPluginVersion
-} from "./chunk-EO2RQW4S.js";
+} from "./chunk-2CKDAFSX.js";
 import {
   findPackageRoot
 } from "./chunk-LPUQPDC2.js";
@@ -91,13 +99,13 @@ import {
   SEARCH_SIMILARITY_THRESHOLD,
   TEAM_SOURCE_PREFIX,
   epochSeconds
-} from "./chunk-CKJAWZQE.js";
+} from "./chunk-W4VHC2ES.js";
 import "./chunk-E7NUADTQ.js";
-import "./chunk-D7TYRPRM.js";
-import "./chunk-E4VLWIJC.js";
+import "./chunk-6LQIMRTC.js";
+import "./chunk-ODXLRR4U.js";
 import {
   external_exports
-} from "./chunk-GDY63YAW.js";
+} from "./chunk-U6PF3YII.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/agent/executor.ts
@@ -110,46 +118,6 @@ import { createSdkMcpServer } from "@anthropic-ai/claude-agent-sdk";
 // src/agent/tools/read-tools.ts
 import { tool } from "@anthropic-ai/claude-agent-sdk";
 
-// src/db/queries/agent-state.ts
-var STATE_COLUMNS = [
-  "agent_id",
-  "key",
-  "value",
-  "updated_at"
-];
-var SELECT_COLUMNS = STATE_COLUMNS.join(", ");
-function toAgentStateRow(row) {
-  return {
-    agent_id: row.agent_id,
-    key: row.key,
-    value: row.value,
-    updated_at: row.updated_at
-  };
-}
-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_COLUMNS} FROM agent_state WHERE agent_id = ? AND key = ?`).get(agentId, key)
-  );
-}
-function getStatesForAgent(agentId) {
-  const db = getDatabase();
-  const rows = db.prepare(
-    `SELECT ${SELECT_COLUMNS}
-     FROM agent_state
-     WHERE agent_id = ?
-     ORDER BY key ASC`
-  ).all(agentId);
-  return rows.map(toAgentStateRow);
-}
-
 // src/agent/tools/types.ts
 function textResult(data) {
   return { content: [{ type: "text", text: JSON.stringify(data) }] };
@@ -245,10 +213,10 @@ function createReadTools(deps) {
   );
   const vaultSearchSemantic = tool(
     "vault_search_semantic",
-    "Semantic similarity search across embedded vault content (spores, sessions, plans, artifacts). Best for finding conceptually related content. Returns results ranked by similarity score.",
+    "Semantic similarity search across embedded vault content (spores, sessions, plans, artifacts, skill_records). Best for finding conceptually related content. Returns results ranked by similarity score.",
     {
       query: external_exports.string().describe("Search query text"),
-      namespace: external_exports.string().optional().describe("Restrict to a content type: spores, sessions, plans, artifacts. Omit to search all."),
+      namespace: external_exports.string().optional().describe("Restrict to a content type: spores, sessions, plans, artifacts, skill_records. Omit to search all."),
       limit: external_exports.number().optional().describe("Maximum results to return")
     },
     async (args) => {
@@ -646,219 +614,8 @@ import crypto2 from "crypto";
 import { readFileSync, writeFileSync, mkdirSync, rmSync, existsSync } from "fs";
 import { resolve } from "path";
 import { tool as tool4 } from "@anthropic-ai/claude-agent-sdk";
-
-// src/agent/tools/skill-validator.ts
-var MAX_SKILL_LINES = 500;
-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 match = fmMatch[1].match(new RegExp(`^${field}:\\s*(.+)$`, "m"));
-  return match?.[1].trim();
-}
-function parseAllowedTools(rawValue) {
-  if (!rawValue) return null;
-  let stripped = rawValue.trim();
-  if (stripped.length === 0) return null;
-  if (stripped.startsWith("[") && stripped.endsWith("]")) {
-    stripped = stripped.slice(1, -1).trim();
-  }
-  if (stripped.length === 0) return null;
-  const parts = stripped.split(",").map((s) => s.trim().replace(/^['"]|['"]$/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;
-}
-function tokenSet(text) {
-  const 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"
-  ]);
-  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 && 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: "${managedMatch[1].trim()}"`);
-  }
-  const allowedToolsMatch = frontmatter.match(/^allowed-tools:\s*(.+)$/m);
-  if (allowedToolsMatch) {
-    const rawValue = allowedToolsMatch[1].trim();
-    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 ${MAX_SKILL_LINES})`);
-  }
-  return issues;
-}
-
-// src/agent/tools/skill-tools.ts
 function createSkillTools(deps) {
-  const { agentId, machineId, projectRoot, vaultDir, recordTurn } = deps;
+  const { agentId, machineId, projectRoot, vaultDir, recordTurn, embeddingManager } = deps;
   function findOverlappingCandidate(newTopic, existing) {
     let best = null;
     for (const candidate of existing) {
@@ -878,7 +635,7 @@ function createSkillTools(deps) {
     const common = `already has an existing candidate with a similar topic: "${match.topic}"`;
     switch (match.status) {
       case CANDIDATE_STATUS.DISMISSED:
-        return `Candidate rejected: the vault ${common} that was previously dismissed. Do not re-identify dismissed topics.`;
+        return `Note: similar to dismissed candidate "${match.topic}". If this is a broader domain that subsumes the dismissed topic, creation is allowed.`;
       case CANDIDATE_STATUS.GENERATED:
         return `Candidate rejected: the vault ${common} that was already fulfilled by a generated skill. Do not re-identify.`;
       case CANDIDATE_STATUS.APPROVED:
@@ -1072,6 +829,7 @@ function createSkillTools(deps) {
       ),
       source_ids: external_exports.string().optional().describe("JSON array of source spore/entity IDs"),
       skill_id: external_exports.string().optional().describe("Associated skill record ID (after materialization)"),
+      supersedes: external_exports.string().optional().describe("JSON array of skill record names this candidate would replace (for domain-level candidates that subsume existing narrow skills)"),
       limit: external_exports.number().optional().describe("Maximum candidates to return (for list)")
     },
     async (args) => {
@@ -1095,9 +853,18 @@ function createSkillTools(deps) {
           if (!args.topic || !args.rationale) {
             return textResult({ error: "topic and rationale are required for create action" });
           }
+          let supersedesNames = [];
+          if (args.supersedes) {
+            try {
+              supersedesNames = JSON.parse(args.supersedes);
+            } catch {
+            }
+          }
+          const supersedesSet = new Set(supersedesNames);
           const activeSkills = listSkillRecords({ agent_id: agentId, status: "active", limit: 100 });
           const topicLower = args.topic.toLowerCase();
           const overlapping = activeSkills.filter((s) => {
+            if (supersedesSet.has(s.name)) return false;
             const nameWords = s.name.split("-").filter((w) => w.length > 2);
             if (nameWords.length < 2) return false;
             return nameWords.every((w) => topicLower.includes(w));
@@ -1110,16 +877,21 @@ function createSkillTools(deps) {
           }
           const allExisting = listCandidates({ agent_id: agentId, limit: 500 });
           const match = findOverlappingCandidate(args.topic, allExisting);
+          let dismissedMatch;
           if (match) {
-            return textResult({
-              error: candidateOverlapError(match.candidate),
-              existing_candidate: {
-                id: match.candidate.id,
-                status: match.candidate.status,
-                topic: match.candidate.topic
-              },
-              similarity: match.score
-            });
+            if (match.candidate.status === CANDIDATE_STATUS.DISMISSED) {
+              dismissedMatch = match;
+            } else {
+              return textResult({
+                error: candidateOverlapError(match.candidate),
+                existing_candidate: {
+                  id: match.candidate.id,
+                  status: match.candidate.status,
+                  topic: match.candidate.topic
+                },
+                similarity: match.score
+              });
+            }
           }
           const now = epochSeconds();
           const candidate = insertCandidate({
@@ -1131,9 +903,18 @@ function createSkillTools(deps) {
             confidence: args.confidence,
             status: args.status,
             source_ids: args.source_ids,
+            supersedes: args.supersedes,
             created_at: now,
             updated_at: now
           });
+          const result = { ...candidate };
+          if (dismissedMatch) {
+            result.warning = candidateOverlapError(dismissedMatch.candidate);
+            result.similar_dismissed_candidate = {
+              id: dismissedMatch.candidate.id,
+              topic: dismissedMatch.candidate.topic
+            };
+          }
           notify(vaultDir, {
             domain: "skills",
             type: "skill.surveyed",
@@ -1142,7 +923,7 @@ function createSkillTools(deps) {
             link: "/skills?tab=candidates",
             metadata: { candidateId: candidate.id, topic: args.topic }
           });
-          return textResult(candidate);
+          return textResult(result);
         }
         case "update": {
           if (!args.id) return textResult({ error: "id is required for update action" });
@@ -1154,6 +935,7 @@ function createSkillTools(deps) {
             ...args.status !== void 0 ? { status: args.status } : {},
             ...args.source_ids !== void 0 ? { source_ids: args.source_ids } : {},
             ...args.skill_id !== void 0 ? { skill_id: args.skill_id } : {},
+            ...args.supersedes !== void 0 ? { supersedes: args.supersedes } : {},
             updated_at: now
           });
           if (!updated) return textResult({ error: `Candidate not found: ${args.id}` });
@@ -1173,7 +955,7 @@ function createSkillTools(deps) {
   );
   const vaultSkillRecords = tool4(
     "vault_skill_records",
-    "Read, update, and delete skill records (materialized skills on disk). Supports list, get, update, and delete actions.",
+    "Read, update, and delete skill records (materialized skills on disk). Supports list, get, update, and delete actions. The get action includes the full SKILL.md file content.",
     {
       action: external_exports.enum(["list", "get", "update", "delete"]).describe("Action to perform"),
       id: external_exports.string().optional().describe("Skill record ID or name (required for get/update/delete)"),
@@ -1198,7 +980,14 @@ function createSkillTools(deps) {
           if (!args.id) return textResult({ error: "id is required for get action" });
           const record = getSkillRecord(args.id) ?? getSkillRecordByName(args.id);
           if (!record) return textResult({ error: `Skill record not found: ${args.id}` });
-          return textResult(record);
+          const result = { ...record };
+          if (record.path && projectRoot) {
+            try {
+              result.content = readFileSync(resolve(projectRoot, record.path), "utf-8");
+            } catch {
+            }
+          }
+          return textResult(result);
         }
         case "update": {
           if (!args.id) return textResult({ error: "id is required for update action" });
@@ -1219,6 +1008,10 @@ function createSkillTools(deps) {
           if (!args.id) return textResult({ error: "id is required for delete action" });
           const result = deleteSkillRecordCascade(args.id);
           if (!result) return textResult({ error: `Skill record not found: ${args.id}` });
+          try {
+            embeddingManager?.onRemoved("skill_records", result.id);
+          } catch {
+          }
           const root = projectRoot ?? process.cwd();
           if (!/[/\\]|\.\./.test(result.name)) {
             const skillDir = resolve(root, ".agents", "skills", result.name);
@@ -1338,6 +1131,11 @@ function createSkillTools(deps) {
           recordId: result.id,
           generation: result.generation
         });
+        embeddingManager?.onContentWritten("skill_records", result.id, args.description, {
+          status: "active",
+          name: args.name
+        }).catch(() => {
+        });
         return textResult(result);
       }
       const priorSkillContent = readFileSync(skillPath, "utf-8");
@@ -1399,6 +1197,11 @@ function createSkillTools(deps) {
         recordId,
         generation
       });
+      embeddingManager?.onContentWritten("skill_records", recordId, args.description, {
+        status: "active",
+        name: args.name
+      }).catch(() => {
+      });
       recordTurn("vault_write_skill", args);
       return textResult({
         id: recordId,
@@ -1538,6 +1341,11 @@ function createSkillTools(deps) {
         recordId: result.id,
         generation: result.generation
       });
+      embeddingManager?.onContentWritten("skill_records", result.id, manifest.description, {
+        status: "active",
+        name: manifest.name
+      }).catch(() => {
+      });
       return textResult(result);
     },
     { annotations: { openWorldHint: true } }
@@ -2595,4 +2403,4 @@ export {
   computeWaves,
   runAgent
 };
-//# sourceMappingURL=executor-NSPRTH4M.js.map
+//# sourceMappingURL=executor-ICTRRUBY.js.map