npm - @goondocks/myco - Versions diffs - 0.9.0 → 0.10.0 - Mend

@goondocks/myco 0.9.0 → 0.10.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (169) hide show

package/dist/ui/index.html CHANGED Viewed

@@ -5,8 +5,8 @@
     <link rel="icon" type="image/svg+xml" href="/favicon.svg" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Myco</title>
-    <script type="module" crossorigin src="/assets/index-DZrElonz.js"></script>
-    <link rel="stylesheet" crossorigin href="/assets/index-TkeiYbZB.css">
+    <script type="module" crossorigin src="/assets/index-CPA_uq_j.js"></script>
+    <link rel="stylesheet" crossorigin href="/assets/index-BGbil7f1.css">
   </head>
   <body>
     <div id="root"></div>

package/dist/update-W3UFZU4G.js ADDED Viewed

@@ -0,0 +1,79 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  VAULT_GITIGNORE
+} from "./chunk-WXSJKESH.js";
+import "./chunk-SAKJMNSR.js";
+import {
+  detectSymbionts
+} from "./chunk-5PEUFJ6U.js";
+import "./chunk-5SDH75YC.js";
+import "./chunk-D7TYRPRM.js";
+import "./chunk-E4VLWIJC.js";
+import "./chunk-KH64DHOY.js";
+import "./chunk-MYX5NCRH.js";
+import "./chunk-YZMNEIFI.js";
+import "./chunk-76ZO5RGT.js";
+import "./chunk-S6I62FAH.js";
+import "./chunk-G2LQBFE3.js";
+import "./chunk-LPUQPDC2.js";
+import {
+  resolveVaultDir
+} from "./chunk-JTYZRPX5.js";
+import "./chunk-PZUWP5VK.js";
+// src/cli/update.ts
+import { execFileSync } from "child_process";
+import fs from "fs";
+import path from "path";
+async function run(args) {
+  const vaultDir = resolveVaultDir();
+  if (!fs.existsSync(path.join(vaultDir, "myco.yaml"))) {
+    console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);
+    process.exit(1);
+  }
+  console.log(`Updating Myco vault at ${vaultDir}
+`);
+  let updatedCount = 0;
+  const gitignorePath = path.join(vaultDir, ".gitignore");
+  const currentGitignore = fs.existsSync(gitignorePath) ? fs.readFileSync(gitignorePath, "utf-8") : "";
+  if (currentGitignore !== VAULT_GITIGNORE) {
+    fs.writeFileSync(gitignorePath, VAULT_GITIGNORE, "utf-8");
+    console.log("  \u2713 Updated .gitignore");
+    updatedCount++;
+  } else {
+    console.log("  \u2013 .gitignore is current");
+  }
+  const projectRoot = path.dirname(vaultDir);
+  const detected = detectSymbionts(projectRoot);
+  if (detected.length > 0) {
+    for (const d of detected) {
+      try {
+        if (d.manifest.pluginInstallCommands.length > 0) {
+          for (const cmd of d.manifest.pluginInstallCommands) {
+            const [bin, ...cmdArgs] = cmd.split(" ");
+            execFileSync(bin, cmdArgs, { stdio: "inherit" });
+          }
+          console.log(`  \u2713 Updated ${d.manifest.displayName} plugin`);
+          updatedCount++;
+        } else {
+          console.log(`  \u2013 ${d.manifest.displayName}: no automated update available`);
+        }
+      } catch (err) {
+        console.error(`  \u2717 Failed to update ${d.manifest.displayName}: ${err.message}`);
+      }
+    }
+  } else {
+    console.log("  \u2013 No agents detected");
+  }
+  console.log("");
+  if (updatedCount > 0) {
+    console.log(`Updated ${updatedCount} item${updatedCount > 1 ? "s" : ""}.`);
+  } else {
+    console.log("Everything is up to date.");
+  }
+  console.log("Run `myco doctor` to verify setup health.");
+}
+export {
+  run
+};
+//# sourceMappingURL=update-W3UFZU4G.js.map

package/dist/update-W3UFZU4G.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"sources":["../src/cli/update.ts"],"sourcesContent":["import { resolveVaultDir } from '../vault/resolve.js';\nimport { VAULT_GITIGNORE } from './shared.js';\nimport { detectSymbionts } from '../symbionts/detect.js';\nimport { execFileSync } from 'node:child_process';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\nexport async function run(args: string[]): Promise<void> {\n const vaultDir = resolveVaultDir();\n if (!fs.existsSync(path.join(vaultDir, 'myco.yaml'))) {\n console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);\n process.exit(1);\n }\n\n console.log(`Updating Myco vault at ${vaultDir}\\n`);\n\n let updatedCount = 0;\n\n // --- Update .gitignore to match current template ---\n\n const gitignorePath = path.join(vaultDir, '.gitignore');\n const currentGitignore = fs.existsSync(gitignorePath)\n ? fs.readFileSync(gitignorePath, 'utf-8')\n : '';\n\n if (currentGitignore !== VAULT_GITIGNORE) {\n fs.writeFileSync(gitignorePath, VAULT_GITIGNORE, 'utf-8');\n console.log(' \\u2713 Updated .gitignore');\n updatedCount++;\n } else {\n console.log(' \\u2013 .gitignore is current');\n }\n\n // --- Update symbiont plugins ---\n\n const projectRoot = path.dirname(vaultDir);\n const detected = detectSymbionts(projectRoot);\n\n if (detected.length > 0) {\n for (const d of detected) {\n try {\n if (d.manifest.pluginInstallCommands.length > 0) {\n for (const cmd of d.manifest.pluginInstallCommands) {\n const [bin, ...cmdArgs] = cmd.split(' ');\n execFileSync(bin, cmdArgs, { stdio: 'inherit' });\n }\n console.log(` \\u2713 Updated ${d.manifest.displayName} plugin`);\n updatedCount++;\n } else {\n console.log(` \\u2013 ${d.manifest.displayName}: no automated update available`);\n }\n } catch (err) {\n console.error(` \\u2717 Failed to update ${d.manifest.displayName}: ${(err as Error).message}`);\n }\n }\n } else {\n console.log(' \\u2013 No agents detected');\n }\n\n // --- Summary ---\n\n console.log('');\n if (updatedCount > 0) {\n console.log(`Updated ${updatedCount} item${updatedCount > 1 ? 's' : ''}.`);\n } else {\n console.log('Everything is up to date.');\n }\n console.log('Run `myco doctor` to verify setup health.');\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;AAGA,SAAS,oBAAoB;AAC7B,OAAO,QAAQ;AACf,OAAO,UAAU;AAEjB,eAAsB,IAAI,MAA+B;AACvD,QAAM,WAAW,gBAAgB;AACjC,MAAI,CAAC,GAAG,WAAW,KAAK,KAAK,UAAU,WAAW,CAAC,GAAG;AACpD,YAAQ,MAAM,yBAAyB,QAAQ,0BAA0B;AACzE,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,UAAQ,IAAI,0BAA0B,QAAQ;AAAA,CAAI;AAElD,MAAI,eAAe;AAInB,QAAM,gBAAgB,KAAK,KAAK,UAAU,YAAY;AACtD,QAAM,mBAAmB,GAAG,WAAW,aAAa,IAChD,GAAG,aAAa,eAAe,OAAO,IACtC;AAEJ,MAAI,qBAAqB,iBAAiB;AACxC,OAAG,cAAc,eAAe,iBAAiB,OAAO;AACxD,YAAQ,IAAI,6BAA6B;AACzC;AAAA,EACF,OAAO;AACL,YAAQ,IAAI,gCAAgC;AAAA,EAC9C;AAIA,QAAM,cAAc,KAAK,QAAQ,QAAQ;AACzC,QAAM,WAAW,gBAAgB,WAAW;AAE5C,MAAI,SAAS,SAAS,GAAG;AACvB,eAAW,KAAK,UAAU;AACxB,UAAI;AACF,YAAI,EAAE,SAAS,sBAAsB,SAAS,GAAG;AAC/C,qBAAW,OAAO,EAAE,SAAS,uBAAuB;AAClD,kBAAM,CAAC,KAAK,GAAG,OAAO,IAAI,IAAI,MAAM,GAAG;AACvC,yBAAa,KAAK,SAAS,EAAE,OAAO,UAAU,CAAC;AAAA,UACjD;AACA,kBAAQ,IAAI,oBAAoB,EAAE,SAAS,WAAW,SAAS;AAC/D;AAAA,QACF,OAAO;AACL,kBAAQ,IAAI,YAAY,EAAE,SAAS,WAAW,iCAAiC;AAAA,QACjF;AAAA,MACF,SAAS,KAAK;AACZ,gBAAQ,MAAM,6BAA6B,EAAE,SAAS,WAAW,KAAM,IAAc,OAAO,EAAE;AAAA,MAChG;AAAA,IACF;AAAA,EACF,OAAO;AACL,YAAQ,IAAI,6BAA6B;AAAA,EAC3C;AAIA,UAAQ,IAAI,EAAE;AACd,MAAI,eAAe,GAAG;AACpB,YAAQ,IAAI,WAAW,YAAY,QAAQ,eAAe,IAAI,MAAM,EAAE,GAAG;AAAA,EAC3E,OAAO;AACL,YAAQ,IAAI,2BAA2B;AAAA,EACzC;AACA,UAAQ,IAAI,2CAA2C;AACzD;","names":[]}

package/dist/{user-prompt-submit-KSM3AR6P.js → user-prompt-submit-LSWCYUW3.js} RENAMED Viewed

@@ -4,13 +4,13 @@ import {
 } from "./chunk-V7XG6V6C.js";
 import {
   readStdin
-} from "./chunk-XNOCTDHF.js";
+} from "./chunk-J4RVYUH4.js";
 import {
   DaemonClient
-} from "./chunk-TRUJLI6K.js";
-import "./chunk-5VZ52A4T.js";
-import "./chunk-WGTCA2NU.js";
-import "./chunk-PB6TOLRQ.js";
+} from "./chunk-YZMNEIFI.js";
+import "./chunk-76ZO5RGT.js";
+import "./chunk-S6I62FAH.js";
+import "./chunk-G2LQBFE3.js";
 import "./chunk-LPUQPDC2.js";
 import {
   resolveVaultDir
@@ -56,4 +56,4 @@ ${sessionLine}` : sessionLine;
 export {
   main
 };
-//# sourceMappingURL=user-prompt-submit-KSM3AR6P.js.map
+//# sourceMappingURL=user-prompt-submit-LSWCYUW3.js.map

package/dist/{verify-UDAYVX37.js → verify-O7TQ5DDY.js} RENAMED Viewed

@@ -1,19 +1,19 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   createEmbeddingProvider
-} from "./chunk-JYOOJCPQ.js";
-import "./chunk-46PWOKSI.js";
-import "./chunk-RJ6ZQKG5.js";
-import "./chunk-KYLDNM7H.js";
-import "./chunk-UBZPD4HN.js";
+} from "./chunk-MKKXCCQ5.js";
+import "./chunk-AEJS57ZK.js";
+import "./chunk-5QERXFH7.js";
+import "./chunk-FPMEIN2W.js";
+import "./chunk-5SDH75YC.js";
 import {
   loadConfig
-} from "./chunk-MHSCMET3.js";
+} from "./chunk-MAZOVVDU.js";
 import "./chunk-D7TYRPRM.js";
 import "./chunk-E4VLWIJC.js";
 import "./chunk-KH64DHOY.js";
-import "./chunk-5VZ52A4T.js";
-import "./chunk-WGTCA2NU.js";
+import "./chunk-76ZO5RGT.js";
+import "./chunk-S6I62FAH.js";
 import "./chunk-PZUWP5VK.js";
 // src/cli/verify.ts
@@ -42,4 +42,4 @@ async function run(_args, vaultDir) {
 export {
   run
 };
-//# sourceMappingURL=verify-UDAYVX37.js.map
+//# sourceMappingURL=verify-O7TQ5DDY.js.map

package/dist/{version-KLBN4HZT.js → version-VWWY7SPQ.js} RENAMED Viewed

@@ -1,10 +1,10 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   getPluginVersion
-} from "./chunk-PB6TOLRQ.js";
+} from "./chunk-G2LQBFE3.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-PZUWP5VK.js";
 export {
   getPluginVersion
 };
-//# sourceMappingURL=version-KLBN4HZT.js.map
+//# sourceMappingURL=version-VWWY7SPQ.js.map

package/dist/version-VWWY7SPQ.js.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@goondocks/myco",
-  "version": "0.9.0",
+  "version": "0.10.0",
   "description": "Collective agent intelligence — Claude Code plugin",
   "type": "module",
   "main": "dist/index.js",

package/dist/chunk-3K5WGSJ4.js.map DELETED Viewed

@@ -1 +0,0 @@

- {"version":3,"sources":["../src/db/queries/spores.ts"],"sourcesContent":["/**\n * Spore CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of spores returned by listSpores when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Default spore status for new spores. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default importance score for new spores. */\nexport const DEFAULT_IMPORTANCE = 5;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a spore. */\nexport interface SporeInsert {\n id: string;\n agent_id: string;\n observation_type: string;\n content: string;\n created_at: number;\n session_id?: string | null;\n prompt_batch_id?: number | null;\n status?: string;\n context?: string | null;\n importance?: number;\n file_path?: string | null;\n tags?: string | null;\n content_hash?: string | null;\n properties?: string | null;\n updated_at?: number | null;\n}\n\n/** Row shape returned from spore queries (all columns). */\nexport interface SporeRow {\n id: string;\n agent_id: string;\n session_id: string | null;\n prompt_batch_id: number | null;\n observation_type: string;\n status: string;\n content: string;\n context: string | null;\n importance: number;\n file_path: string | null;\n tags: string | null;\n content_hash: string | null;\n properties: string | null;\n embedded: number;\n created_at: number;\n updated_at: number | null;\n}\n\n/** Filter options for `listSpores`. */\nexport interface ListSporesOptions {\n agent_id?: string;\n observation_type?: string;\n status?: string;\n session_id?: string;\n search?: string;\n limit?: number;\n offset?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst SPORE_COLUMNS = [\n 'id',\n 'agent_id',\n 'session_id',\n 'prompt_batch_id',\n 'observation_type',\n 'status',\n 'content',\n 'context',\n 'importance',\n 'file_path',\n 'tags',\n 'content_hash',\n 'properties',\n 'embedded',\n 'created_at',\n 'updated_at',\n] as const;\n\nconst SELECT_COLUMNS = SPORE_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed SporeRow. */\nfunction toSporeRow(row: Record<string, unknown>): SporeRow {\n return {\n id: row.id as string,\n agent_id: row.agent_id as string,\n session_id: (row.session_id as string) ?? null,\n prompt_batch_id: (row.prompt_batch_id as number) ?? null,\n observation_type: row.observation_type as string,\n status: row.status as string,\n content: row.content as string,\n context: (row.context as string) ?? null,\n importance: row.importance as number,\n file_path: (row.file_path as string) ?? null,\n tags: (row.tags as string) ?? null,\n content_hash: (row.content_hash as string) ?? null,\n properties: (row.properties as string) ?? null,\n embedded: (row.embedded as number) ?? 0,\n created_at: row.created_at as number,\n updated_at: (row.updated_at as number) ?? null,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new spore.\n *\n * Requires a valid `agent_id` (foreign key to agents table).\n */\nexport function insertSpore(data: SporeInsert): SporeRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO spores (\n id, agent_id, session_id, prompt_batch_id,\n observation_type, status, content, context,\n importance, file_path, tags, content_hash,\n properties, created_at, updated_at\n ) VALUES (\n ?, ?, ?, ?,\n ?, ?, ?, ?,\n ?, ?, ?, ?,\n ?, ?, ?\n )`,\n ).run(\n data.id,\n data.agent_id,\n data.session_id ?? null,\n data.prompt_batch_id ?? null,\n data.observation_type,\n data.status ?? DEFAULT_STATUS,\n data.content,\n data.context ?? null,\n data.importance ?? DEFAULT_IMPORTANCE,\n data.file_path ?? null,\n data.tags ?? null,\n data.content_hash ?? null,\n data.properties ?? null,\n data.created_at,\n data.updated_at ?? null,\n );\n\n return toSporeRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM spores WHERE id = ?`).get(data.id) as Record<string, unknown>,\n );\n}\n\n/**\n * Retrieve a single spore by id.\n *\n * @returns the spore row, or null if not found.\n */\nexport function getSpore(id: string): SporeRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM spores WHERE id = ?`,\n ).get(id) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toSporeRow(row);\n}\n\n/**\n * List spores with optional filters, ordered by created_at DESC.\n */\n/** Build WHERE clause and bound params from spore filter options. */\nfunction buildSporeWhere(\n options: Omit<ListSporesOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.agent_id !== undefined) {\n conditions.push(`agent_id = ?`);\n params.push(options.agent_id);\n }\n if (options.observation_type !== undefined) {\n conditions.push(`observation_type = ?`);\n params.push(options.observation_type);\n }\n if (options.status !== undefined) {\n conditions.push(`status = ?`);\n params.push(options.status);\n }\n if (options.session_id !== undefined) {\n conditions.push(`session_id = ?`);\n params.push(options.session_id);\n }\n if (options.search !== undefined && options.search.length > 0) {\n conditions.push(`(content LIKE ? OR observation_type LIKE ?)`);\n const pattern = `%${options.search}%`;\n params.push(pattern, pattern);\n }\n\n return {\n where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n params,\n };\n}\n\n/**\n * List spores with optional filters, ordered by created_at DESC.\n */\nexport function listSpores(\n options: ListSporesOptions = {},\n): SporeRow[] {\n const db = getDatabase();\n const { where, params } = buildSporeWhere(options);\n const limit = options.limit ?? 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- {"version":3,"sources":["../src/db/queries/sessions.ts"],"sourcesContent":["/**\n * Session CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of sessions returned by listSessions when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Session status value when a session is closed normally. */\nconst STATUS_COMPLETED = 'completed';\n\n/** Default session status for new sessions. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default prompt count for new sessions. */\nconst DEFAULT_PROMPT_COUNT = 0;\n\n/** Default tool count for new sessions. */\nconst DEFAULT_TOOL_COUNT = 0;\n\n/** Default processed flag for new sessions. */\nconst DEFAULT_PROCESSED = 0;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting/upserting a session. */\nexport interface SessionInsert {\n id: string;\n agent: string;\n started_at: number;\n created_at: number;\n user?: string | null;\n project_root?: string | null;\n branch?: string | null;\n ended_at?: number | null;\n status?: string;\n prompt_count?: number;\n tool_count?: number;\n title?: string | null;\n summary?: string | null;\n transcript_path?: string | null;\n parent_session_id?: string | null;\n parent_session_reason?: string | null;\n processed?: number;\n content_hash?: string | null;\n}\n\n/** Row shape returned from session queries (all columns). */\nexport interface SessionRow {\n id: string;\n agent: string;\n user: string | null;\n project_root: string | null;\n branch: string | null;\n started_at: number;\n ended_at: number | null;\n status: string;\n prompt_count: number;\n tool_count: number;\n title: string | null;\n summary: string | null;\n transcript_path: string | null;\n parent_session_id: string | null;\n parent_session_reason: string | null;\n processed: number;\n content_hash: string | null;\n embedded: number;\n created_at: number;\n}\n\n/** Updatable fields for `updateSession`. */\nexport interface SessionUpdate {\n agent?: string;\n user?: string | null;\n project_root?: string | null;\n branch?: string | null;\n ended_at?: number | null;\n status?: string;\n prompt_count?: number;\n tool_count?: number;\n title?: string | null;\n summary?: string | null;\n transcript_path?: string | null;\n parent_session_id?: string | null;\n parent_session_reason?: string | null;\n processed?: number;\n content_hash?: string | null;\n}\n\n/** Filter options for `listSessions`. */\nexport interface ListSessionsOptions {\n limit?: number;\n offset?: number;\n status?: string;\n agent?: string;\n search?: string;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst SESSION_COLUMNS = [\n 'id',\n 'agent',\n '\"user\"',\n 'project_root',\n 'branch',\n 'started_at',\n 'ended_at',\n 'status',\n 'prompt_count',\n 'tool_count',\n 'title',\n 'summary',\n 'transcript_path',\n 'parent_session_id',\n 'parent_session_reason',\n 'processed',\n 'content_hash',\n 'embedded',\n 'created_at',\n] as const;\n\nconst SELECT_COLUMNS = SESSION_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Normalize a SQLite result row into a typed SessionRow.\n *\n * The quoted \"user\" column comes back as `user` in the result object.\n */\nfunction toSessionRow(row: Record<string, unknown>): SessionRow {\n return {\n id: row.id as string,\n agent: row.agent as string,\n user: (row.user as string) ?? null,\n project_root: (row.project_root as string) ?? null,\n branch: (row.branch as string) ?? null,\n started_at: row.started_at as number,\n ended_at: (row.ended_at as number) ?? null,\n status: row.status as string,\n prompt_count: row.prompt_count as number,\n tool_count: row.tool_count as number,\n title: (row.title as string) ?? null,\n summary: (row.summary as string) ?? null,\n transcript_path: (row.transcript_path as string) ?? null,\n parent_session_id: (row.parent_session_id as string) ?? null,\n parent_session_reason: (row.parent_session_reason as string) ?? null,\n processed: row.processed as number,\n content_hash: (row.content_hash as string) ?? null,\n embedded: (row.embedded as number) ?? 0,\n created_at: row.created_at as number,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a session or update it if the id already exists.\n *\n * On conflict the row is updated with the values from `data`, preserving\n * any columns not supplied via COALESCE with EXCLUDED values.\n */\nexport function upsertSession(data: SessionInsert): SessionRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO sessions (\n id, agent, \"user\", project_root, branch,\n started_at, ended_at, status, prompt_count, tool_count,\n title, summary, transcript_path,\n parent_session_id, parent_session_reason,\n processed, content_hash, created_at\n ) VALUES (\n ?, ?, ?, ?, ?,\n ?, ?, ?, ?, ?,\n ?, ?, ?,\n ?, ?,\n ?, ?, ?\n )\n ON CONFLICT (id) DO UPDATE SET\n agent = EXCLUDED.agent,\n \"user\" = EXCLUDED.\"user\",\n project_root = EXCLUDED.project_root,\n branch = EXCLUDED.branch,\n started_at = EXCLUDED.started_at,\n ended_at = COALESCE(EXCLUDED.ended_at, sessions.ended_at),\n status = COALESCE(EXCLUDED.status, sessions.status),\n prompt_count = CASE WHEN ? THEN EXCLUDED.prompt_count ELSE sessions.prompt_count END,\n tool_count = CASE WHEN ? THEN EXCLUDED.tool_count ELSE sessions.tool_count END,\n title = COALESCE(EXCLUDED.title, sessions.title),\n summary = COALESCE(EXCLUDED.summary, sessions.summary),\n transcript_path = COALESCE(EXCLUDED.transcript_path, sessions.transcript_path),\n parent_session_id = EXCLUDED.parent_session_id,\n parent_session_reason = EXCLUDED.parent_session_reason,\n processed = COALESCE(EXCLUDED.processed, sessions.processed),\n content_hash = EXCLUDED.content_hash`,\n ).run(\n data.id,\n data.agent,\n data.user ?? null,\n data.project_root ?? null,\n data.branch ?? null,\n data.started_at,\n data.ended_at ?? null,\n data.status ?? DEFAULT_STATUS,\n data.prompt_count ?? DEFAULT_PROMPT_COUNT,\n data.tool_count ?? DEFAULT_TOOL_COUNT,\n data.title ?? null,\n data.summary ?? null,\n data.transcript_path ?? null,\n data.parent_session_id ?? null,\n data.parent_session_reason ?? null,\n data.processed ?? DEFAULT_PROCESSED,\n data.content_hash ?? null,\n data.created_at,\n data.prompt_count !== undefined ? 1 : 0,\n data.tool_count !== undefined ? 1 : 0,\n );\n\n return toSessionRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`).get(data.id) as Record<string, unknown>,\n );\n}\n\n/**\n * Retrieve a single session by id.\n *\n * @returns the session row, or null if not found.\n */\nexport function getSession(id: string): SessionRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`,\n ).get(id) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toSessionRow(row);\n}\n\n/** Build WHERE clause and bound params from session filter options. */\nfunction buildSessionsWhere(\n options: Omit<ListSessionsOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.status !== undefined) {\n conditions.push(`status = ?`);\n params.push(options.status);\n }\n\n if (options.agent !== undefined) {\n conditions.push(`agent = ?`);\n params.push(options.agent);\n }\n\n if (options.search !== undefined && options.search.length > 0) {\n conditions.push(`(title LIKE ? OR id LIKE ?)`);\n const pattern = `%${options.search}%`;\n params.push(pattern, pattern);\n }\n\n return {\n where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n params,\n };\n}\n\n/**\n * List sessions with optional filters, ordered by created_at DESC.\n */\nexport function listSessions(\n options: ListSessionsOptions = {},\n): SessionRow[] {\n const db = getDatabase();\n const { where, params } = buildSessionsWhere(options);\n const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n const offset = options.offset ?? 0;\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM sessions\n ${where}\n ORDER BY created_at DESC\n LIMIT ?\n OFFSET ?`,\n ).all(...params, limit, offset) as Record<string, unknown>[];\n\n return rows.map(toSessionRow);\n}\n\n/**\n * Count sessions matching optional filters (for pagination totals).\n */\nexport function countSessions(\n options: Omit<ListSessionsOptions, 'limit' | 'offset'> = {},\n): number {\n const db = getDatabase();\n const { where, params } = buildSessionsWhere(options);\n\n const row = db.prepare(\n `SELECT COUNT(*) as count FROM sessions ${where}`,\n ).get(...params) as { count: number };\n\n return row.count;\n}\n\n/**\n * Update specific fields on an existing session.\n *\n * @returns the updated row, or null if the session does not exist.\n */\nexport function updateSession(\n id: string,\n updates: SessionUpdate,\n): SessionRow | null {\n const db = getDatabase();\n\n const setClauses: string[] = [];\n const params: unknown[] = [];\n\n const fieldMap: Record<string, string> = {\n agent: 'agent',\n user: '\"user\"',\n project_root: 'project_root',\n branch: 'branch',\n ended_at: 'ended_at',\n status: 'status',\n prompt_count: 'prompt_count',\n tool_count: 'tool_count',\n title: 'title',\n summary: 'summary',\n transcript_path: 'transcript_path',\n parent_session_id: 'parent_session_id',\n parent_session_reason: 'parent_session_reason',\n processed: 'processed',\n content_hash: 'content_hash',\n };\n\n for (const [key, column] of Object.entries(fieldMap)) {\n if (key in updates) {\n setClauses.push(`${column} = ?`);\n params.push((updates as Record<string, unknown>)[key] ?? null);\n }\n }\n\n if (setClauses.length === 0) return getSession(id);\n\n params.push(id);\n\n db.prepare(\n `UPDATE sessions\n SET ${setClauses.join(', ')}\n WHERE id = ?`,\n ).run(...params);\n\n return getSession(id);\n}\n\n/**\n * Close a session — set status to 'completed' and record the end time.\n *\n * @returns the updated row, or null if the session does not exist.\n */\nexport function closeSession(\n id: string,\n endedAt: number,\n): SessionRow | null {\n const db = getDatabase();\n\n db.prepare(\n `UPDATE sessions\n SET status = ?, ended_at = ?\n WHERE id = ?`,\n ).run(STATUS_COMPLETED, endedAt, id);\n\n return getSession(id);\n}\n\n/**\n * Delete a session and all its child rows (batches, activities, attachments).\n *\n * No ON DELETE CASCADE in the schema, so we delete children first.\n * Returns true if the session existed and was deleted.\n */\nexport function deleteSession(id: string): boolean {\n const db = getDatabase();\n\n db.prepare(`DELETE FROM activities WHERE session_id = ?`).run(id);\n db.prepare(`DELETE FROM attachments WHERE session_id = ?`).run(id);\n db.prepare(`DELETE FROM prompt_batches WHERE session_id = ?`).run(id);\n const info = db.prepare(`DELETE FROM sessions WHERE id = ?`).run(id);\n\n return info.changes > 0;\n}\n\n// ---------------------------------------------------------------------------\n// Cascade delete + impact query\n// ---------------------------------------------------------------------------\n\n/** Counts of related data that would be affected by a session delete. */\nexport interface SessionImpact {\n promptCount: number;\n sporeCount: number;\n attachmentCount: number;\n graphEdgeCount: number;\n}\n\n/** Result of a cascade delete operation. */\nexport interface DeleteCascadeResult {\n deleted: boolean;\n counts: {\n prompts: number;\n spores: number;\n attachments: number;\n graphEdges: number;\n resolutionEvents: number;\n };\n /** Spore IDs that were deleted (needed for vault file + vector cleanup). */\n deletedSporeIds: string[];\n /** Attachment file paths that were deleted from DB (needed for disk cleanup). */\n deletedAttachmentPaths: string[];\n}\n\n/**\n * Get counts of all data related to a session, for pre-delete impact display.\n */\nexport function getSessionImpact(sessionId: string): SessionImpact {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT\n (SELECT COUNT(*) FROM prompt_batches WHERE session_id = ?) AS promptCount,\n (SELECT COUNT(*) FROM spores WHERE session_id = ?) AS sporeCount,\n (SELECT COUNT(*) FROM attachments WHERE session_id = ?) AS attachmentCount,\n (SELECT COUNT(*) FROM graph_edges WHERE session_id = ?) AS graphEdgeCount`,\n ).get(sessionId, sessionId, sessionId, sessionId) as SessionImpact;\n\n return row;\n}\n\n/**\n * Delete a session and ALL related data in a single transaction.\n *\n * Returns counts of deleted rows and IDs needed for post-transaction\n * cleanup (vault files, embedding vectors).\n */\nexport function deleteSessionCascade(sessionId: string): DeleteCascadeResult {\n const db = getDatabase();\n\n const zeroCounts: DeleteCascadeResult = {\n deleted: false,\n counts: { prompts: 0, spores: 0, attachments: 0, graphEdges: 0, resolutionEvents: 0 },\n deletedSporeIds: [],\n deletedAttachmentPaths: [],\n };\n\n // Check session exists first\n const exists = db.prepare(`SELECT id FROM sessions WHERE id = ?`).get(sessionId);\n if (!exists) return zeroCounts;\n\n // Collect IDs/paths needed for post-transaction cleanup before deleting\n const sporeIds = (db.prepare(\n `SELECT id FROM spores WHERE session_id = ?`,\n ).all(sessionId) as { id: string }[]).map((r) => r.id);\n\n 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- {"version":3,"sources":["../src/db/schema.ts"],"sourcesContent":["/**\n * SQLite database schema -- all capture, intelligence, and agent state tables.\n *\n * Uses `CREATE TABLE IF NOT EXISTS` and `CREATE INDEX IF NOT EXISTS` throughout\n * for idempotency. Running `createSchema()` multiple times is always safe.\n *\n * Timestamp convention: all timestamps are INTEGER (Unix epoch seconds).\n * Content hashing: all `content_hash` columns are TEXT with UNIQUE constraint.\n * Embedding dimensions: 1024 (bge-m3 default) -- used by external sqlite-vec store.\n *\n * Vector columns live in a separate sqlite-vec virtual table, not inline.\n * Tables that participate in vector search carry an `embedded INTEGER DEFAULT 0`\n * flag so the embedder knows which rows still need vectors.\n */\n\nimport type { Database } from 'better-sqlite3';\nimport { epochSeconds } from '@myco/constants.js';\n\n/** Current schema version -- fresh start for the SQLite era. */\nexport const SCHEMA_VERSION = 3;\n\n/** Embedding vector dimensions (bge-m3 default). */\nexport const EMBEDDING_DIMENSIONS = 1024;\n\n// ---------------------------------------------------------------------------\n// DDL statements\n// ---------------------------------------------------------------------------\n\nconst SCHEMA_VERSION_TABLE = `\n CREATE TABLE IF NOT EXISTS schema_version (\n version INTEGER PRIMARY KEY,\n applied_at INTEGER NOT NULL\n )`;\n\n// -- Capture Layer ----------------------------------------------------------\n\nconst SESSIONS_TABLE = `\n CREATE TABLE IF NOT EXISTS sessions (\n id TEXT PRIMARY KEY,\n agent TEXT NOT NULL,\n \"user\" TEXT,\n project_root TEXT,\n branch TEXT,\n started_at INTEGER NOT NULL,\n ended_at INTEGER,\n status TEXT DEFAULT 'active',\n prompt_count INTEGER DEFAULT 0,\n tool_count INTEGER DEFAULT 0,\n title TEXT,\n summary TEXT,\n transcript_path TEXT,\n parent_session_id TEXT,\n parent_session_reason TEXT,\n processed INTEGER DEFAULT 0,\n content_hash TEXT UNIQUE,\n created_at INTEGER NOT NULL,\n embedded INTEGER DEFAULT 0\n )`;\n\nconst PROMPT_BATCHES_TABLE = `\n CREATE TABLE IF NOT EXISTS prompt_batches (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n session_id TEXT NOT NULL REFERENCES sessions(id),\n prompt_number INTEGER,\n user_prompt TEXT,\n response_summary TEXT,\n classification TEXT,\n started_at INTEGER,\n ended_at INTEGER,\n status TEXT DEFAULT 'active',\n activity_count INTEGER DEFAULT 0,\n processed INTEGER DEFAULT 0,\n content_hash TEXT UNIQUE,\n created_at INTEGER NOT NULL\n )`;\n\nconst ACTIVITIES_TABLE = `\n CREATE TABLE IF NOT EXISTS activities (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n session_id TEXT NOT NULL REFERENCES sessions(id),\n prompt_batch_id INTEGER REFERENCES prompt_batches(id),\n tool_name TEXT NOT NULL,\n tool_input TEXT,\n tool_output_summary TEXT,\n file_path TEXT,\n files_affected TEXT,\n duration_ms INTEGER,\n success INTEGER DEFAULT 1,\n error_message TEXT,\n timestamp INTEGER NOT NULL,\n processed INTEGER DEFAULT 0,\n content_hash TEXT UNIQUE,\n created_at INTEGER NOT NULL\n )`;\n\nconst PLANS_TABLE = `\n CREATE TABLE IF NOT EXISTS plans (\n id TEXT PRIMARY KEY,\n status TEXT DEFAULT 'active',\n author TEXT,\n title TEXT,\n content TEXT,\n source_path TEXT,\n tags TEXT,\n session_id TEXT REFERENCES sessions(id),\n prompt_batch_id INTEGER REFERENCES prompt_batches(id),\n content_hash TEXT,\n processed INTEGER DEFAULT 0,\n created_at INTEGER NOT NULL,\n updated_at INTEGER,\n embedded INTEGER DEFAULT 0\n )`;\n\nconst ARTIFACTS_TABLE = `\n CREATE TABLE IF NOT EXISTS artifacts (\n id TEXT PRIMARY KEY,\n artifact_type TEXT,\n source_path TEXT NOT NULL,\n title TEXT NOT NULL,\n content TEXT,\n last_captured_by TEXT,\n tags TEXT,\n created_at INTEGER NOT NULL,\n updated_at INTEGER,\n embedded INTEGER DEFAULT 0\n )`;\n\nconst TEAM_MEMBERS_TABLE = `\n CREATE TABLE IF NOT EXISTS team_members (\n id TEXT PRIMARY KEY,\n \"user\" TEXT NOT NULL,\n role TEXT,\n joined TEXT,\n tags TEXT\n )`;\n\nconst ATTACHMENTS_TABLE = `\n CREATE TABLE IF NOT EXISTS attachments (\n id TEXT PRIMARY KEY,\n session_id TEXT REFERENCES sessions(id),\n prompt_batch_id INTEGER REFERENCES prompt_batches(id),\n file_path TEXT NOT NULL,\n media_type TEXT,\n description TEXT,\n data BLOB,\n content_hash TEXT,\n created_at INTEGER NOT NULL\n )`;\n\n// -- Intelligence Layer -----------------------------------------------------\n\nconst AGENTS_TABLE = `\n CREATE TABLE IF NOT EXISTS agents (\n id TEXT PRIMARY KEY,\n name TEXT NOT NULL,\n provider TEXT,\n model TEXT,\n system_prompt_hash TEXT,\n config TEXT,\n source TEXT NOT NULL DEFAULT 'built-in',\n system_prompt TEXT,\n max_turns INTEGER,\n timeout_seconds INTEGER,\n tool_access TEXT,\n enabled INTEGER NOT NULL DEFAULT 1,\n created_at INTEGER NOT NULL,\n updated_at INTEGER\n )`;\n\nconst SPORES_TABLE = `\n CREATE TABLE IF NOT EXISTS spores (\n id TEXT PRIMARY KEY,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n session_id TEXT REFERENCES sessions(id),\n prompt_batch_id INTEGER REFERENCES prompt_batches(id),\n observation_type TEXT NOT NULL,\n status TEXT DEFAULT 'active',\n content TEXT NOT NULL,\n context TEXT,\n importance INTEGER DEFAULT 5,\n file_path 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entities(id),\n note_id TEXT NOT NULL,\n note_type TEXT NOT NULL,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n UNIQUE (entity_id, note_id, note_type, agent_id)\n )`;\n\nconst RESOLUTION_EVENTS_TABLE = `\n CREATE TABLE IF NOT EXISTS resolution_events (\n id TEXT PRIMARY KEY,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n spore_id TEXT NOT NULL REFERENCES spores(id),\n action TEXT NOT NULL,\n new_spore_id TEXT,\n reason TEXT,\n session_id TEXT,\n created_at INTEGER NOT NULL\n )`;\n\nconst DIGEST_EXTRACTS_TABLE = `\n CREATE TABLE IF NOT EXISTS digest_extracts (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n tier INTEGER NOT NULL,\n content TEXT NOT NULL,\n substrate_hash TEXT,\n generated_at INTEGER NOT NULL,\n UNIQUE (agent_id, tier)\n )`;\n\n// -- Agent State Layer ------------------------------------------------------\n\nconst AGENT_RUNS_TABLE = `\n CREATE TABLE IF NOT EXISTS agent_runs (\n id TEXT PRIMARY KEY,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n task TEXT,\n instruction TEXT,\n status TEXT DEFAULT 'pending',\n started_at INTEGER,\n completed_at INTEGER,\n tokens_used INTEGER,\n cost_usd REAL,\n actions_taken TEXT,\n error TEXT\n )`;\n\nconst AGENT_REPORTS_TABLE = `\n CREATE TABLE IF NOT EXISTS agent_reports (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n run_id TEXT NOT NULL REFERENCES agent_runs(id),\n agent_id TEXT NOT NULL REFERENCES agents(id),\n action TEXT NOT NULL,\n summary TEXT NOT NULL,\n details TEXT,\n created_at INTEGER NOT NULL\n )`;\n\nconst AGENT_TURNS_TABLE = `\n CREATE TABLE IF NOT EXISTS agent_turns (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n run_id TEXT NOT NULL REFERENCES agent_runs(id),\n agent_id TEXT NOT NULL REFERENCES agents(id),\n turn_number INTEGER NOT NULL,\n tool_name TEXT NOT NULL,\n tool_input TEXT,\n tool_output_summary TEXT,\n started_at INTEGER,\n completed_at INTEGER\n )`;\n\nconst AGENT_TASKS_TABLE = `\n CREATE TABLE IF NOT EXISTS agent_tasks (\n id TEXT PRIMARY KEY,\n agent_id TEXT NOT NULL REFERENCES agents(id),\n source TEXT NOT NULL DEFAULT 'built-in',\n display_name TEXT,\n description TEXT,\n prompt TEXT NOT NULL,\n is_default INTEGER DEFAULT 0,\n tool_overrides TEXT,\n model TEXT,\n config TEXT,\n created_at INTEGER NOT NULL,\n updated_at INTEGER\n )`;\n\nconst AGENT_STATE_TABLE = `\n CREATE TABLE IF NOT EXISTS agent_state (\n agent_id TEXT NOT NULL REFERENCES agents(id),\n key TEXT NOT NULL,\n value TEXT NOT NULL,\n updated_at INTEGER NOT NULL,\n PRIMARY KEY (agent_id, key)\n )`;\n\n// -- Logging Layer ----------------------------------------------------------\n\nconst LOG_ENTRIES_TABLE = `\n CREATE TABLE IF NOT EXISTS log_entries (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n timestamp TEXT NOT NULL,\n level TEXT NOT NULL,\n component TEXT NOT NULL,\n kind TEXT NOT NULL,\n message TEXT NOT NULL,\n data TEXT,\n session_id TEXT\n )`;\n\n// -- FTS5 Virtual Tables ----------------------------------------------------\n\nconst FTS_TABLES = [\n `CREATE VIRTUAL TABLE IF NOT EXISTS prompt_batches_fts\n USING fts5(user_prompt, content='prompt_batches', content_rowid='id')`,\n\n `CREATE VIRTUAL TABLE IF NOT EXISTS activities_fts\n USING fts5(tool_name, tool_input, file_path, content='activities', content_rowid='id')`,\n\n `CREATE VIRTUAL TABLE IF NOT EXISTS log_entries_fts\n USING fts5(message, content='log_entries', content_rowid='id')`,\n\n // FTS5 sync triggers for log_entries (external-content table)\n `CREATE TRIGGER IF NOT EXISTS log_entries_ai AFTER INSERT ON log_entries BEGIN\n INSERT INTO log_entries_fts(rowid, message) VALUES (new.id, new.message);\n END`,\n\n `CREATE TRIGGER IF NOT EXISTS log_entries_ad AFTER DELETE ON log_entries BEGIN\n INSERT INTO log_entries_fts(log_entries_fts, rowid, message) VALUES('delete', old.id, old.message);\n END`,\n];\n\n// -- Indexes ----------------------------------------------------------------\n\nconst SECONDARY_INDEXES = [\n // Sessions\n 'CREATE INDEX IF NOT EXISTS idx_sessions_status ON sessions (status)',\n 'CREATE INDEX IF NOT EXISTS idx_sessions_processed ON sessions (processed)',\n 'CREATE INDEX IF NOT EXISTS idx_sessions_started_at ON sessions (started_at)',\n 'CREATE INDEX IF NOT EXISTS idx_sessions_agent ON sessions (agent)',\n\n // Prompt batches\n 'CREATE INDEX IF NOT EXISTS idx_prompt_batches_session_id ON prompt_batches (session_id)',\n 'CREATE INDEX IF NOT EXISTS idx_prompt_batches_processed ON prompt_batches (processed)',\n 'CREATE INDEX IF NOT EXISTS idx_prompt_batches_status ON prompt_batches (status)',\n\n // Activities\n 'CREATE INDEX IF NOT EXISTS idx_activities_session_id ON activities (session_id)',\n 'CREATE INDEX IF NOT EXISTS idx_activities_prompt_batch_id ON activities (prompt_batch_id)',\n 'CREATE INDEX IF NOT EXISTS idx_activities_tool_name ON activities (tool_name)',\n 'CREATE INDEX IF NOT EXISTS idx_activities_timestamp ON activities (timestamp)',\n 'CREATE INDEX IF NOT EXISTS idx_activities_processed ON activities (processed)',\n\n // Spores\n 'CREATE INDEX IF NOT EXISTS idx_spores_agent_id ON spores (agent_id)',\n 'CREATE INDEX IF NOT EXISTS idx_spores_session_id ON spores (session_id)',\n 'CREATE INDEX IF NOT EXISTS idx_spores_status ON spores (status)',\n 'CREATE INDEX IF NOT EXISTS idx_spores_observation_type ON spores (observation_type)',\n 'CREATE INDEX IF NOT EXISTS idx_spores_created_at ON spores (created_at)',\n\n // Entities\n 'CREATE INDEX IF NOT EXISTS idx_entities_agent_id ON entities (agent_id)',\n 'CREATE INDEX IF NOT EXISTS idx_entities_type ON entities (type)',\n\n // Graph edges\n 'CREATE INDEX IF NOT EXISTS idx_graph_edges_source ON graph_edges (source_id, source_type)',\n 'CREATE INDEX IF NOT EXISTS idx_graph_edges_target ON graph_edges (target_id, target_type)',\n 'CREATE INDEX IF NOT EXISTS idx_graph_edges_type ON graph_edges (type)',\n 'CREATE INDEX IF NOT EXISTS idx_graph_edges_agent ON graph_edges (agent_id)',\n 'CREATE INDEX IF NOT EXISTS idx_graph_edges_source_type ON graph_edges (source_id, type)',\n\n // Entity mentions\n 'CREATE INDEX IF NOT EXISTS idx_entity_mentions_entity_id ON entity_mentions (entity_id)',\n 'CREATE INDEX IF NOT EXISTS idx_entity_mentions_agent_id ON entity_mentions (agent_id)',\n\n // Resolution events\n 'CREATE INDEX IF NOT EXISTS idx_resolution_events_spore_id ON resolution_events (spore_id)',\n 'CREATE INDEX IF NOT EXISTS idx_resolution_events_agent_id ON resolution_events (agent_id)',\n\n // Digest extracts\n 'CREATE INDEX IF NOT EXISTS idx_digest_extracts_agent_id ON digest_extracts (agent_id)',\n\n // Agent runs\n 'CREATE INDEX IF NOT EXISTS idx_agent_runs_agent_id ON agent_runs (agent_id)',\n 'CREATE INDEX IF NOT EXISTS idx_agent_runs_status ON agent_runs (status)',\n 'CREATE INDEX IF NOT EXISTS idx_agent_runs_agent_status ON agent_runs (agent_id, status)',\n\n // Agent reports\n 'CREATE INDEX IF NOT EXISTS idx_agent_reports_run_id ON agent_reports (run_id)',\n\n // Agent turns\n 'CREATE INDEX IF NOT EXISTS idx_agent_turns_run_id ON agent_turns (run_id)',\n\n // Agent tasks\n 'CREATE INDEX IF NOT EXISTS idx_agent_tasks_agent_id ON agent_tasks (agent_id)',\n\n // Plans\n 'CREATE INDEX IF NOT EXISTS idx_plans_session_id ON plans (session_id)',\n 'CREATE INDEX IF NOT EXISTS idx_plans_source_path ON plans (source_path)',\n 'CREATE INDEX IF NOT EXISTS idx_plans_content_hash ON plans (content_hash)',\n // Attachments\n 'CREATE INDEX IF NOT EXISTS idx_attachments_file_path ON attachments (file_path)',\n\n // Log entries\n 'CREATE INDEX IF NOT EXISTS idx_log_entries_timestamp ON log_entries (timestamp)',\n 'CREATE INDEX IF NOT EXISTS idx_log_entries_level ON log_entries (level)',\n 'CREATE INDEX IF NOT EXISTS idx_log_entries_component ON log_entries (component)',\n 'CREATE INDEX IF NOT EXISTS idx_log_entries_kind ON log_entries (kind)',\n 'CREATE INDEX IF NOT EXISTS idx_log_entries_session_id ON log_entries (session_id)',\n];\n\n// -- Ordered table creation -------------------------------------------------\n\nconst TABLE_DDLS = [\n SCHEMA_VERSION_TABLE,\n // Capture layer (order matters for FK references)\n SESSIONS_TABLE,\n PROMPT_BATCHES_TABLE,\n ACTIVITIES_TABLE,\n PLANS_TABLE,\n ARTIFACTS_TABLE,\n TEAM_MEMBERS_TABLE,\n ATTACHMENTS_TABLE,\n // Intelligence layer\n AGENTS_TABLE,\n SPORES_TABLE,\n ENTITIES_TABLE,\n GRAPH_EDGES_TABLE,\n ENTITY_MENTIONS_TABLE,\n RESOLUTION_EVENTS_TABLE,\n DIGEST_EXTRACTS_TABLE,\n // Agent state layer\n AGENT_RUNS_TABLE,\n AGENT_REPORTS_TABLE,\n AGENT_TURNS_TABLE,\n AGENT_TASKS_TABLE,\n AGENT_STATE_TABLE,\n // Logging layer\n LOG_ENTRIES_TABLE,\n];\n\n// ---------------------------------------------------------------------------\n// Migrations\n// ---------------------------------------------------------------------------\n\n/**\n * Migrate a version-1 database to version-2.\n *\n * Version 2 adds:\n * - plans.session_id, plans.prompt_batch_id, plans.content_hash\n * - attachments.data, 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(session_id)',\n 'CREATE INDEX IF NOT EXISTS idx_plans_source_path ON plans (source_path)',\n 'CREATE INDEX IF NOT EXISTS idx_plans_content_hash ON plans (content_hash)',\n 'CREATE INDEX IF NOT EXISTS idx_attachments_file_path ON attachments (file_path)',\n ];\n\n for (const idx of newIndexes) {\n db.exec(idx);\n }\n\n db.prepare(\n `INSERT INTO schema_version (version, applied_at)\n VALUES (?, ?)\n ON CONFLICT (version) DO NOTHING`\n ).run(2, epochSeconds());\n\n db.exec('COMMIT');\n } catch (err) {\n db.exec('ROLLBACK');\n throw err;\n }\n}\n\n/**\n * Migrate a version-2 database to version-3.\n *\n * Version 3 adds:\n * - log_entries table\n * - log_entries_fts virtual table (FTS5)\n * - indexes: idx_log_entries_timestamp, _level, _component, _kind, _session_id\n *\n * Uses `CREATE ... 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- {"version":3,"sources":["../src/config/loader.ts","../src/config/schema.ts","../src/config/migrations.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport YAML from 'yaml';\nimport { MycoConfigSchema, type MycoConfig } from './schema.js';\nimport { runMigrations, CURRENT_MIGRATION_VERSION } from './migrations.js';\n\nexport const CONFIG_FILENAME = 'myco.yaml';\n\nexport function loadConfig(vaultDir: string): MycoConfig {\n const configPath = path.join(vaultDir, CONFIG_FILENAME);\n\n if (!fs.existsSync(configPath)) {\n throw new Error(`myco.yaml not found in ${vaultDir}`);\n }\n\n const raw = fs.readFileSync(configPath, 'utf-8');\n const parsed = YAML.parse(raw) as Record<string, unknown>;\n\n // Detect v1 config and guide migration\n if (parsed.version === 1 || (parsed.intelligence as Record<string, unknown>)?.backend) {\n throw new Error(\n 'Myco config uses v1 format. Run /myco:setup-llm to reconfigure for v2.',\n );\n }\n\n // --- v2 → v3 migration ---\n let v2Migrated = false;\n if (parsed.version === 2) {\n // Extract intelligence.embedding to top-level embedding\n const intel = parsed.intelligence as Record<string, unknown> | undefined;\n const embeddingConfig = intel?.embedding as Record<string, unknown> | undefined;\n if (embeddingConfig && !parsed.embedding) {\n // Map v2 'lm-studio' to v3 'openai-compatible' for embedding provider\n if (embeddingConfig.provider === 'lm-studio') {\n embeddingConfig.provider = 'openai-compatible';\n }\n parsed.embedding = embeddingConfig;\n }\n\n // Keep daemon.port and daemon.log_level, drop grace_period and max_log_size\n const daemon = parsed.daemon as Record<string, unknown> | undefined;\n if (daemon) {\n const { port, log_level } = daemon;\n parsed.daemon = { port: port ?? null, log_level: log_level ?? 'info' };\n }\n\n // Keep capture basics, drop token-related fields; migrate artifact_watch → plan_dirs\n const capture = parsed.capture as Record<string, unknown> | undefined;\n if (capture) {\n const { transcript_paths, artifact_watch, plan_dirs, artifact_extensions, buffer_max_events } = capture;\n parsed.capture = {\n transcript_paths,\n plan_dirs: plan_dirs ?? artifact_watch,\n artifact_extensions,\n buffer_max_events,\n };\n }\n\n // Drop removed top-level sections\n delete parsed.intelligence;\n delete parsed.context;\n delete parsed.team;\n delete parsed.digest;\n delete parsed.pipeline;\n\n // Set version to 3\n parsed.version = 3;\n v2Migrated = true;\n\n process.stderr.write('[myco migration] Migrated config from v2 to v3\\n');\n }\n\n // Run numbered migrations (for v3+ forward migrations)\n const migrationsRan = runMigrations(parsed, vaultDir, (msg) => {\n process.stderr.write(`[myco migration] ${msg}\\n`);\n });\n\n // Parse with Zod to fill in defaults for new config 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ProviderOverrideSchema = z.object({\n type: z.enum(['cloud', 'ollama', 'lmstudio']),\n base_url: z.string().optional(),\n model: z.string().optional(),\n /** Context window size for local models (Ollama num_ctx, LM Studio context_length). */\n context_length: z.number().int().positive().optional(),\n});\n\n/** Per-phase overrides within a task — keyed by phase name. */\nconst PhaseOverrideSchema = z.object({\n provider: ProviderOverrideSchema.optional(),\n model: z.string().optional(),\n maxTurns: z.number().int().positive().optional(),\n});\n\n/** Per-task config override — stored in myco.yaml under agent.tasks. */\nconst TaskProviderOverrideSchema = z.object({\n provider: ProviderOverrideSchema.optional(),\n model: z.string().optional(),\n maxTurns: z.number().int().positive().optional(),\n timeoutSeconds: z.number().int().positive().optional(),\n phases: z.record(z.string(), PhaseOverrideSchema).optional(),\n});\n\nconst ContextSchema = z.object({\n /** Which digest tier to inject 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TaskProviderOverrideSchema>;\nexport type PhaseOverride = z.infer<typeof PhaseOverrideSchema>;\nexport type ContextConfig = z.infer<typeof ContextSchema>;\n","/**\n * Config and vault migrations — run once per version, tracked by config_version.\n *\n * Each migration has a version number, a name, and a function that receives\n * the raw parsed YAML doc and the vault directory. 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- {"version":3,"sources":["../src/db/queries/batches.ts","../src/utils/error-message.ts","../src/db/queries/turns.ts","../src/db/queries/runs.ts","../src/db/queries/reports.ts","../src/db/queries/graph-edges.ts","../src/db/queries/lineage.ts","../src/db/queries/entities.ts","../src/db/queries/digest-extracts.ts"],"sourcesContent":["/**\n * Prompt batch CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of unprocessed batches returned when no limit given. */\nconst DEFAULT_UNPROCESSED_LIMIT = 100;\n\n/** Default number of batches returned by listBatchesBySession when no limit given. */\nexport const BATCHES_DEFAULT_LIMIT = 200;\n\n/** Batch status value when a batch is closed normally. */\nconst STATUS_COMPLETED = 'completed';\n\n/** Default batch status for new batches. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default activity count for new batches. */\nconst DEFAULT_ACTIVITY_COUNT = 0;\n\n/** Default processed flag for new batches. */\nconst DEFAULT_PROCESSED = 0;\n\n/** Processed flag value indicating a batch has been processed. */\nconst PROCESSED_FLAG = 1;\n\n/** Number of characters used for prompt prefix matching. */\nconst PROMPT_PREFIX_MATCH_CHARS = 60;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Filter options for `listBatchesBySession`. */\nexport interface ListBatchesBySessionOptions {\n limit?: number;\n offset?: number;\n}\n\n/** Fields required (or optional) when inserting a prompt batch. */\nexport interface BatchInsert {\n session_id: string;\n created_at: number;\n prompt_number?: number | null;\n user_prompt?: string | null;\n response_summary?: string | null;\n classification?: string | null;\n started_at?: number | null;\n ended_at?: number | null;\n status?: string;\n activity_count?: number;\n processed?: number;\n content_hash?: string | null;\n}\n\n/** Row shape returned from batch queries. */\nexport interface BatchRow {\n id: number;\n session_id: string;\n prompt_number: number | null;\n user_prompt: string | null;\n response_summary: string | null;\n classification: string | null;\n started_at: number | null;\n ended_at: number | null;\n status: string;\n activity_count: number;\n processed: number;\n content_hash: string | null;\n created_at: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst BATCH_COLUMNS = [\n 'id',\n 'session_id',\n 'prompt_number',\n 'user_prompt',\n 'response_summary',\n 'classification',\n 'started_at',\n 'ended_at',\n 'status',\n 'activity_count',\n 'processed',\n 'content_hash',\n 'created_at',\n] as const;\n\nconst SELECT_COLUMNS = BATCH_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed BatchRow. */\nfunction toBatchRow(row: Record<string, unknown>): BatchRow {\n return {\n id: row.id as number,\n session_id: row.session_id as string,\n prompt_number: (row.prompt_number as number) ?? 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null,\n data.user_prompt ?? null,\n data.response_summary ?? null,\n data.classification ?? null,\n data.started_at ?? null,\n data.ended_at ?? null,\n data.status ?? DEFAULT_STATUS,\n data.activity_count ?? DEFAULT_ACTIVITY_COUNT,\n data.processed ?? DEFAULT_PROCESSED,\n data.content_hash ?? null,\n data.created_at,\n );\n\n const batchId = Number(info.lastInsertRowid);\n\n // FTS5 sync\n const userPrompt = data.user_prompt ?? null;\n if (userPrompt) {\n db.prepare('INSERT INTO prompt_batches_fts(rowid, user_prompt) VALUES (?, ?)').run(batchId, userPrompt);\n }\n\n return toBatchRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM prompt_batches WHERE id = ?`).get(batchId) as Record<string, unknown>,\n );\n}\n\n/**\n * Close a batch — set status to 'completed' and record the end time.\n *\n * @returns the updated row, or null if the batch does not exist.\n */\nexport function closeBatch(\n id: number,\n endedAt: number,\n): BatchRow | null {\n const db = getDatabase();\n\n const info = db.prepare(\n `UPDATE prompt_batches\n SET status = ?, ended_at = ?\n WHERE id = ?`,\n ).run(STATUS_COMPLETED, endedAt, id);\n\n if (info.changes === 0) return null;\n\n return toBatchRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM prompt_batches WHERE id = ?`).get(id) as Record<string, unknown>,\n );\n}\n\n/**\n * Populate response_summary on batches from transcript turns.\n *\n * Matches transcript turns (ordered by position) to batches (ordered by id ASC).\n * This is resilient to prompt_number duplicates caused by daemon restarts.\n * Only updates batches that don't already have a response_summary.\n *\n * @param sessionId — the session to update\n * @param responses — array of { response } ordered by turn position (1-indexed)\n */\nexport function populateBatchResponses(\n sessionId: string,\n responses: Array<{ turnIndex: number; response: string }>,\n): void {\n const db = getDatabase();\n\n // Get all batches for this session ordered by id (insertion order = true order)\n const batches = db.prepare(\n `SELECT id FROM prompt_batches WHERE session_id = ? ORDER BY id ASC`,\n ).all(sessionId) as Array<{ id: number }>;\n\n // Map each response to the batch at the same position\n for (const { turnIndex, response } of responses) {\n const batchIndex = turnIndex - 1; // turns are 1-indexed\n if (batchIndex >= 0 && batchIndex < batches.length) {\n const batchId = batches[batchIndex].id;\n db.prepare(\n `UPDATE prompt_batches SET response_summary = ? WHERE id = ? AND response_summary IS NULL`,\n ).run(response, batchId);\n }\n }\n}\n\n/**\n * Get unprocessed batches, ordered by id ASC (insertion order).\n *\n * Supports cursor-based pagination via `after_id` and a `limit` cap.\n */\nexport function getUnprocessedBatches(\n options: { after_id?: number; limit?: number } = {},\n): BatchRow[] {\n const db = getDatabase();\n\n const conditions: string[] = [`processed = ?`];\n const params: unknown[] = [DEFAULT_PROCESSED];\n\n if (options.after_id !== undefined) {\n conditions.push(`id > ?`);\n params.push(options.after_id);\n }\n\n const limit = options.limit ?? DEFAULT_UNPROCESSED_LIMIT;\n params.push(limit);\n\n const where = conditions.join(' AND ');\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM prompt_batches\n WHERE ${where}\n ORDER BY id ASC\n LIMIT ?`,\n ).all(...params) as Record<string, unknown>[];\n\n return rows.map(toBatchRow);\n}\n\n/**\n * Increment the activity_count for a batch by 1.\n *\n * @returns the updated row, or null if the batch does not exist.\n */\nexport function incrementActivityCount(\n id: number,\n): BatchRow | null {\n const db = getDatabase();\n\n const info = db.prepare(\n `UPDATE prompt_batches\n SET activity_count = activity_count + 1\n WHERE id = ?`,\n ).run(id);\n\n if (info.changes === 0) return null;\n\n return toBatchRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM prompt_batches WHERE id = ?`).get(id) as Record<string, unknown>,\n );\n}\n\n/**\n * Mark a batch as processed (processed = 1).\n *\n * @returns the updated row, or null if the batch does not exist.\n */\nexport function markBatchProcessed(\n id: number,\n): BatchRow | null {\n const db = getDatabase();\n\n const info = db.prepare(\n `UPDATE prompt_batches\n SET processed = ?\n WHERE id = ?`,\n ).run(PROCESSED_FLAG, id);\n\n if (info.changes === 0) return null;\n\n return toBatchRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM prompt_batches WHERE id = ?`).get(id) as Record<string, unknown>,\n );\n}\n\n/**\n * Get a batch's ID by session and prompt number.\n * Used to link attachments to their prompt batch at stop time.\n */\nexport function getBatchIdByPromptNumber(\n sessionId: string,\n promptNumber: number,\n): number | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT id FROM prompt_batches WHERE session_id = ? AND prompt_number = ? LIMIT 1`,\n ).get(sessionId, promptNumber) as { id: number } | undefined;\n\n return row ? row.id : null;\n}\n\n/**\n * Find a batch by matching the start of its user_prompt text.\n * Used for attachment matching after transcript compaction where turn indices no longer\n * align with prompt_numbers.\n */\nexport function findBatchByPromptPrefix(\n sessionId: string,\n promptPrefix: string,\n): { id: number; prompt_number: number } | null {\n const db = getDatabase();\n // Match first N chars — enough to be unique, tolerant of minor differences\n const prefix = promptPrefix.slice(0, PROMPT_PREFIX_MATCH_CHARS);\n const row = db.prepare(\n `SELECT id, prompt_number FROM prompt_batches\n WHERE session_id = ? AND user_prompt LIKE ? || '%'\n LIMIT 1`,\n ).get(sessionId, prefix) as { id: number; prompt_number: number } | undefined;\n return row ?? null;\n}\n\n/** Fields required when inserting a batch statelessly (prompt_number derived from DB). */\nexport interface StatelessBatchInsert {\n session_id: string;\n created_at: number;\n user_prompt?: string | null;\n started_at?: number | null;\n status?: string;\n}\n\n/**\n * Insert a new prompt batch with prompt_number derived from an inline subquery.\n *\n * The prompt_number is set to `COALESCE(MAX(prompt_number), 0) + 1` for the\n * session, so the caller never needs a separate SELECT. This makes the insert\n * stateless — no in-memory counter required.\n *\n * FTS5 index is kept in sync via a follow-up INSERT into prompt_batches_fts.\n */\nexport function insertBatchStateless(data: StatelessBatchInsert): BatchRow {\n const db = getDatabase();\n\n const info = db.prepare(\n `INSERT INTO prompt_batches (\n session_id, prompt_number, user_prompt, response_summary,\n classification, started_at, ended_at, status,\n activity_count, processed, content_hash, created_at\n ) VALUES (\n ?,\n (SELECT COALESCE(MAX(prompt_number), 0) + 1 FROM prompt_batches WHERE session_id = ?),\n ?, NULL,\n NULL, ?, NULL, ?,\n ?, ?, NULL, ?\n )`,\n ).run(\n data.session_id,\n data.session_id,\n data.user_prompt ?? null,\n data.started_at ?? null,\n data.status ?? DEFAULT_STATUS,\n DEFAULT_ACTIVITY_COUNT,\n DEFAULT_PROCESSED,\n data.created_at,\n );\n\n const batchId = Number(info.lastInsertRowid);\n\n // FTS5 sync\n const userPrompt = data.user_prompt ?? null;\n if (userPrompt) {\n db.prepare('INSERT INTO prompt_batches_fts(rowid, user_prompt) VALUES (?, ?)').run(batchId, userPrompt);\n }\n\n return toBatchRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM prompt_batches WHERE id = ?`).get(batchId) as Record<string, unknown>,\n );\n}\n\n/**\n * Close all open batches for a session — blind UPDATE, no prior SELECT needed.\n *\n * Sets `status = 'completed'` and `ended_at` on every batch that has no\n * `ended_at` value yet. Returns the number of batches closed.\n */\nexport function closeOpenBatches(\n sessionId: string,\n endedAt: number,\n): number {\n const db = getDatabase();\n\n const info = db.prepare(\n `UPDATE prompt_batches\n SET status = ?, ended_at = ?\n WHERE session_id = ? AND ended_at IS NULL`,\n ).run(STATUS_COMPLETED, endedAt, sessionId);\n\n return info.changes;\n}\n\n/**\n * Set response_summary on a batch if it doesn't already have one.\n *\n * Idempotent — only updates NULL response_summary.\n */\nexport function setResponseSummary(\n batchId: number,\n summary: string,\n): void {\n const db = getDatabase();\n db.prepare(\n `UPDATE prompt_batches SET response_summary = ? WHERE id = ? AND response_summary IS NULL`,\n ).run(summary, batchId);\n}\n\n/**\n * Get the most recent batch for a session (by id DESC), regardless of status.\n *\n * Used by processStopEvent to attach the AI response and images to the\n * correct batch without positional turn mapping.\n */\nexport function getLatestBatch(\n sessionId: string,\n): BatchRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM prompt_batches\n WHERE session_id = ?\n ORDER BY id DESC LIMIT 1`,\n ).get(sessionId) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toBatchRow(row);\n}\n\nexport function listBatchesBySession(\n sessionId: string,\n options: ListBatchesBySessionOptions = {},\n): BatchRow[] {\n const db = getDatabase();\n\n const limit = options.limit ?? BATCHES_DEFAULT_LIMIT;\n const offset = options.offset ?? 0;\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM prompt_batches\n WHERE session_id = ?\n ORDER BY prompt_number ASC\n LIMIT ?\n OFFSET ?`,\n ).all(sessionId, limit, offset) as Record<string, unknown>[];\n\n return rows.map(toBatchRow);\n}\n","/**\n * Extract a human-readable error message from an unknown thrown value.\n *\n * Handles Error instances, strings, and arbitrary objects. Never throws.\n */\nexport function errorMessage(err: unknown): string {\n if (err instanceof Error) return err.message || err.constructor.name || 'Error';\n if (typeof err === 'string') return err || 'Empty string error';\n try { return JSON.stringify(err); } catch { return 'Unserializable error'; }\n}\n","/**\n * Agent turn CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a turn. */\nexport interface TurnInsert {\n run_id: string;\n agent_id: string;\n turn_number: number;\n tool_name: string;\n tool_input?: string | null;\n tool_output_summary?: string | null;\n started_at?: number | null;\n completed_at?: number | null;\n}\n\n/** Row shape returned from agent_turns queries (all columns). */\nexport interface TurnRow {\n id: number;\n run_id: string;\n agent_id: string;\n turn_number: number;\n tool_name: string;\n tool_input: string | null;\n tool_output_summary: string | null;\n started_at: number | null;\n completed_at: number | null;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst TURN_COLUMNS = [\n 'id',\n 'run_id',\n 'agent_id',\n 'turn_number',\n 'tool_name',\n 'tool_input',\n 'tool_output_summary',\n 'started_at',\n 'completed_at',\n] as const;\n\nconst SELECT_COLUMNS = TURN_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed TurnRow. */\nfunction toTurnRow(row: Record<string, unknown>): TurnRow {\n return {\n id: row.id as number,\n run_id: row.run_id as string,\n agent_id: row.agent_id as string,\n turn_number: row.turn_number as number,\n tool_name: row.tool_name as string,\n tool_input: (row.tool_input as string) ?? null,\n tool_output_summary: (row.tool_output_summary as string) ?? null,\n started_at: (row.started_at as number) ?? null,\n completed_at: (row.completed_at as number) ?? null,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new agent turn.\n *\n * The `id` is auto-generated by the INTEGER PRIMARY KEY (AUTOINCREMENT).\n */\nexport function insertTurn(data: TurnInsert): TurnRow {\n const db = getDatabase();\n\n const info = db.prepare(\n `INSERT INTO agent_turns (\n run_id, agent_id, turn_number, tool_name,\n tool_input, tool_output_summary, started_at, completed_at\n ) VALUES (\n ?, ?, ?, ?,\n ?, ?, ?, ?\n )`,\n ).run(\n data.run_id,\n data.agent_id,\n data.turn_number,\n data.tool_name,\n data.tool_input ?? null,\n data.tool_output_summary ?? null,\n data.started_at ?? null,\n data.completed_at ?? null,\n );\n\n const turnId = Number(info.lastInsertRowid);\n\n return toTurnRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_turns WHERE id = ?`).get(turnId) as Record<string, unknown>,\n );\n}\n\n/**\n * List all turns for a specific run, ordered by turn_number ASC.\n */\nexport function listTurns(runId: string): TurnRow[] {\n const db = getDatabase();\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM agent_turns\n WHERE run_id = ?\n ORDER BY turn_number ASC`,\n ).all(runId) as Record<string, unknown>[];\n\n return rows.map(toTurnRow);\n}\n\n/**\n * List all agent turns for a run, ordered by turn_number ASC.\n *\n * Alias for `listTurns` with an explicit \"by run\" naming convention used\n * by the dashboard API layer.\n */\nexport function listTurnsByRun(runId: string): TurnRow[] {\n return listTurns(runId);\n}\n","/**\n * Agent run CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of runs returned by listRuns when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Default run status for new runs. */\nconst DEFAULT_STATUS = 'pending';\n\n/** Run status indicating the run is currently executing. */\nexport const STATUS_RUNNING = 'running';\n\n/** Run status for a successfully completed run. */\nexport const STATUS_COMPLETED = 'completed';\n\n/** Run status for a run that encountered an error. */\nexport const STATUS_FAILED = 'failed';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a run. */\nexport interface RunInsert {\n id: string;\n agent_id: string;\n task?: string | null;\n instruction?: string | null;\n status?: string;\n started_at?: number | null;\n completed_at?: number | null;\n tokens_used?: number | null;\n cost_usd?: number | null;\n actions_taken?: string | null;\n error?: string | null;\n}\n\n/** Row shape returned from agent_runs queries (all columns). */\nexport interface RunRow {\n id: string;\n agent_id: string;\n task: string | null;\n instruction: string | null;\n status: string;\n started_at: number | null;\n completed_at: number | null;\n tokens_used: number | null;\n cost_usd: number | null;\n actions_taken: string | null;\n error: string | null;\n}\n\n/** Completion data passed to updateRunStatus. */\nexport interface RunCompletion {\n completed_at?: number;\n tokens_used?: number;\n cost_usd?: number;\n actions_taken?: string;\n error?: string;\n}\n\n/** Filter options for `listRuns`. */\nexport interface ListRunsOptions {\n limit?: number;\n offset?: number;\n agent_id?: string;\n status?: string;\n task?: string;\n search?: string;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst RUN_COLUMNS = [\n 'id',\n 'agent_id',\n 'task',\n 'instruction',\n 'status',\n 'started_at',\n 'completed_at',\n 'tokens_used',\n 'cost_usd',\n 'actions_taken',\n 'error',\n] as const;\n\nconst SELECT_COLUMNS = RUN_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed RunRow. */\nfunction toRunRow(row: Record<string, unknown>): RunRow {\n return {\n id: row.id as string,\n agent_id: row.agent_id as string,\n task: (row.task as string) ?? null,\n instruction: (row.instruction as string) ?? null,\n status: row.status as string,\n started_at: (row.started_at as number) ?? null,\n completed_at: (row.completed_at as number) ?? null,\n tokens_used: (row.tokens_used as number) ?? null,\n cost_usd: (row.cost_usd as number) ?? null,\n actions_taken: (row.actions_taken as string) ?? null,\n error: (row.error as string) ?? null,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new agent run.\n */\nexport function insertRun(data: RunInsert): RunRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO agent_runs (\n id, agent_id, task, instruction, status,\n started_at, completed_at, tokens_used, cost_usd,\n actions_taken, error\n ) VALUES (\n ?, ?, ?, ?, ?,\n ?, ?, ?, ?,\n ?, ?\n )`,\n ).run(\n data.id,\n data.agent_id,\n data.task ?? null,\n data.instruction ?? null,\n data.status ?? DEFAULT_STATUS,\n data.started_at ?? null,\n data.completed_at ?? null,\n data.tokens_used ?? null,\n data.cost_usd ?? null,\n data.actions_taken ?? null,\n data.error ?? null,\n );\n\n return toRunRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`).get(data.id) as Record<string, unknown>,\n );\n}\n\n/**\n * Retrieve a single run by id.\n *\n * @returns the run row, or null if not found.\n */\nexport function getRun(id: string): RunRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`,\n ).get(id) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toRunRow(row);\n}\n\n/** Build a WHERE clause and params array from ListRunsOptions filter fields. */\nfunction buildRunsWhere(\n options: Omit<ListRunsOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.agent_id !== undefined) {\n conditions.push(`agent_id = ?`);\n params.push(options.agent_id);\n }\n if (options.status !== undefined) {\n conditions.push(`status = ?`);\n params.push(options.status);\n }\n if (options.task !== undefined) {\n conditions.push(`task = ?`);\n params.push(options.task);\n }\n if (options.search !== undefined && options.search.length > 0) {\n conditions.push(`task LIKE ?`);\n params.push(`%${options.search}%`);\n }\n\n return {\n where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n params,\n };\n}\n\n/**\n * List runs with optional filters, ordered by started_at DESC (nulls last).\n */\nexport function listRuns(\n options: ListRunsOptions = {},\n): RunRow[] {\n const db = getDatabase();\n const { where, params } = buildRunsWhere(options);\n const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n const offset = options.offset ?? 0;\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM agent_runs\n ${where}\n ORDER BY started_at DESC NULLS LAST\n LIMIT ?\n OFFSET ?`,\n ).all(...params, limit, offset) as Record<string, unknown>[];\n\n return rows.map(toRunRow);\n}\n\n/**\n * Count runs matching the given filters (no limit/offset).\n */\nexport function countRuns(\n options: Omit<ListRunsOptions, 'limit' | 'offset'> = {},\n): number {\n const db = getDatabase();\n const { where, params } = buildRunsWhere(options);\n\n const row = db.prepare(\n `SELECT COUNT(*) as count FROM agent_runs ${where}`,\n ).get(...params) as { count: number };\n\n return row.count;\n}\n\n/**\n * Update a run's status, with optional completion data.\n *\n * @returns the updated row, or null if the run does not exist.\n */\nexport function updateRunStatus(\n id: string,\n status: string,\n completion?: RunCompletion,\n): RunRow | null {\n const db = getDatabase();\n\n const setClauses: string[] = ['status = ?'];\n const params: unknown[] = [status];\n\n if (completion?.completed_at !== undefined) {\n setClauses.push(`completed_at = ?`);\n params.push(completion.completed_at);\n }\n\n if (completion?.tokens_used !== undefined) {\n setClauses.push(`tokens_used = ?`);\n params.push(completion.tokens_used);\n }\n\n if (completion?.cost_usd !== undefined) {\n setClauses.push(`cost_usd = ?`);\n params.push(completion.cost_usd);\n }\n\n if (completion?.actions_taken !== undefined) {\n setClauses.push(`actions_taken = ?`);\n params.push(completion.actions_taken);\n }\n\n if (completion?.error !== undefined) {\n setClauses.push(`error = ?`);\n params.push(completion.error);\n }\n\n params.push(id);\n\n const info = db.prepare(\n `UPDATE agent_runs\n SET ${setClauses.join(', ')}\n WHERE id = ?`,\n ).run(...params);\n\n if (info.changes === 0) return null;\n\n return toRunRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_runs WHERE id = ?`).get(id) as Record<string, unknown>,\n );\n}\n\n/**\n * Get the currently running run for an agent, if any.\n *\n * @returns the running run row, or null if no run is active.\n */\nexport function getRunningRun(\n agentId: string,\n): RunRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM agent_runs\n WHERE agent_id = ? AND status = ?\n ORDER BY started_at DESC NULLS LAST\n LIMIT 1`,\n ).get(agentId, STATUS_RUNNING) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toRunRow(row);\n}\n","/**\n * Agent report CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of reports returned by list queries when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a report. */\nexport interface ReportInsert {\n run_id: string;\n agent_id: string;\n action: string;\n summary: string;\n details?: string | null;\n created_at: number;\n}\n\n/** Row shape returned from agent_reports queries (all columns). */\nexport interface ReportRow {\n id: number;\n run_id: string;\n agent_id: string;\n action: string;\n summary: string;\n details: string | null;\n created_at: number;\n}\n\n/** Filter options for `listReportsByAgent`. */\nexport interface ListReportsByAgentOptions {\n limit?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst REPORT_COLUMNS = [\n 'id',\n 'run_id',\n 'agent_id',\n 'action',\n 'summary',\n 'details',\n 'created_at',\n] as const;\n\nconst SELECT_COLUMNS = REPORT_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed ReportRow. */\nfunction toReportRow(row: Record<string, unknown>): ReportRow {\n return {\n id: row.id as number,\n run_id: row.run_id as string,\n agent_id: row.agent_id as string,\n action: row.action as string,\n summary: row.summary as string,\n details: (row.details as string) ?? null,\n created_at: row.created_at as number,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new agent report.\n *\n * The `id` is auto-generated by the INTEGER PRIMARY KEY (AUTOINCREMENT).\n */\nexport function insertReport(data: ReportInsert): ReportRow {\n const db = getDatabase();\n\n const info = db.prepare(\n `INSERT INTO agent_reports (\n run_id, agent_id, action, summary, details, created_at\n ) VALUES (\n ?, ?, ?, ?, ?, ?\n )`,\n ).run(\n data.run_id,\n data.agent_id,\n data.action,\n data.summary,\n data.details ?? null,\n data.created_at,\n );\n\n const reportId = Number(info.lastInsertRowid);\n\n return toReportRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_reports WHERE id = ?`).get(reportId) as Record<string, unknown>,\n );\n}\n\n/**\n * List all reports for a specific run, ordered by created_at ASC.\n */\nexport function listReports(runId: string): ReportRow[] {\n const db = getDatabase();\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM agent_reports\n WHERE run_id = ?\n ORDER BY created_at ASC`,\n ).all(runId) as Record<string, unknown>[];\n\n return rows.map(toReportRow);\n}\n\n/**\n * List reports by agent, ordered by created_at DESC.\n */\nexport function listReportsByAgent(\n agentId: string,\n options: ListReportsByAgentOptions = {},\n): ReportRow[] {\n const db = getDatabase();\n\n const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM agent_reports\n WHERE agent_id = ?\n ORDER BY created_at DESC\n LIMIT ?`,\n ).all(agentId, limit) as Record<string, unknown>[];\n\n return rows.map(toReportRow);\n}\n","/**\n * Graph edge CRUD query helpers.\n *\n * Unlike the `edges` table (which has FK constraints to entities), `graph_edges`\n * supports edges between any node types (session, batch, spore, entity).\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport crypto from 'node:crypto';\nimport { getDatabase } from '@myco/db/client.js';\nimport { QUERY_DEFAULT_LIST_LIMIT, GRAPH_EDGE_DEFAULT_CONFIDENCE } from '@myco/constants.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default BFS traversal depth. */\nconst DEFAULT_BFS_DEPTH = 2;\n\n/** Maximum BFS traversal depth (capped for performance). */\nconst MAX_BFS_DEPTH = 5;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Valid node types in the graph. */\nexport type GraphNodeType = 'session' | 'batch' | 'spore' | 'entity';\n\n/** Lineage edge types (auto-created by daemon, no LLM). */\nexport type LineageEdgeType = 'FROM_SESSION' | 'EXTRACTED_FROM' | 'DERIVED_FROM' | 'HAS_BATCH';\n\n/** Semantic edge types (created by intelligence agent, LLM-driven). */\nexport type SemanticEdgeType = 'RELATES_TO' | 'SUPERSEDED_BY' | 'REFERENCES' | 'DEPENDS_ON' | 'AFFECTS';\n\n/** All valid graph edge types. */\nexport type GraphEdgeType = LineageEdgeType | SemanticEdgeType;\n\n/** Fields required (or optional) when inserting a graph edge. */\nexport interface GraphEdgeInsert {\n agent_id: string;\n source_id: string;\n source_type: GraphNodeType;\n target_id: string;\n target_type: GraphNodeType;\n type: GraphEdgeType;\n created_at: number;\n session_id?: string;\n confidence?: number;\n properties?: string;\n}\n\n/** Row shape returned from graph edge queries. */\nexport interface GraphEdgeRow {\n id: string;\n agent_id: string;\n source_id: string;\n source_type: string;\n target_id: string;\n target_type: string;\n type: string;\n session_id: string | null;\n confidence: number;\n properties: string | null;\n created_at: number;\n}\n\n/** Filter options for `listGraphEdges`. */\nexport interface ListGraphEdgesOptions {\n sourceId?: string;\n targetId?: string;\n type?: string;\n agentId?: string;\n limit?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst GRAPH_EDGE_COLUMNS = [\n 'id',\n 'agent_id',\n 'source_id',\n 'source_type',\n 'target_id',\n 'target_type',\n 'type',\n 'session_id',\n 'confidence',\n 'properties',\n 'created_at',\n] as const;\n\nconst SELECT_COLUMNS = GRAPH_EDGE_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed GraphEdgeRow. */\nfunction toGraphEdgeRow(row: Record<string, unknown>): GraphEdgeRow {\n return {\n id: row.id as string,\n agent_id: row.agent_id as string,\n source_id: row.source_id as string,\n source_type: row.source_type as string,\n target_id: row.target_id as string,\n target_type: row.target_type as string,\n type: row.type as string,\n session_id: (row.session_id as string) ?? null,\n confidence: row.confidence as number,\n properties: (row.properties as string) ?? null,\n created_at: row.created_at as number,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new graph edge.\n *\n * Generates a UUID id automatically.\n */\nexport function insertGraphEdge(data: GraphEdgeInsert): GraphEdgeRow {\n const db = getDatabase();\n const id = crypto.randomUUID();\n\n db.prepare(\n `INSERT INTO graph_edges (\n id, agent_id, source_id, source_type, target_id, target_type,\n type, session_id, confidence, properties, created_at\n ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,\n ).run(\n id,\n data.agent_id,\n data.source_id,\n data.source_type,\n data.target_id,\n data.target_type,\n data.type,\n data.session_id ?? null,\n data.confidence ?? GRAPH_EDGE_DEFAULT_CONFIDENCE,\n data.properties ?? null,\n data.created_at,\n );\n\n return toGraphEdgeRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM graph_edges WHERE id = ?`).get(id) as Record<string, unknown>,\n );\n}\n\n/**\n * List graph edges with optional filters, ordered by created_at DESC.\n */\nexport function listGraphEdges(\n options: ListGraphEdgesOptions = {},\n): GraphEdgeRow[] {\n const db = getDatabase();\n\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.sourceId !== undefined) {\n conditions.push(`source_id = ?`);\n params.push(options.sourceId);\n }\n\n if (options.targetId !== undefined) {\n conditions.push(`target_id = ?`);\n params.push(options.targetId);\n }\n\n if (options.type !== undefined) {\n conditions.push(`type = ?`);\n params.push(options.type);\n }\n\n if (options.agentId !== undefined) {\n conditions.push(`agent_id = ?`);\n params.push(options.agentId);\n }\n\n const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n const limit = options.limit ?? QUERY_DEFAULT_LIST_LIMIT;\n\n params.push(limit);\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM graph_edges\n ${where}\n ORDER BY created_at DESC\n LIMIT ?`,\n ).all(...params) as Record<string, unknown>[];\n\n return rows.map(toGraphEdgeRow);\n}\n\n/**\n * BFS traversal from a node across graph edges.\n *\n * Returns all edges reachable within `depth` hops from the starting node.\n *\n * @param nodeId - The starting node ID.\n * @param nodeType - The starting node type.\n * @param options - Optional depth limit (default 2, max 5).\n */\nexport function getGraphForNode(\n nodeId: string,\n nodeType: GraphNodeType,\n options?: { depth?: number },\n): { edges: GraphEdgeRow[] } {\n const db = getDatabase();\n const depth = Math.min(Math.max(options?.depth ?? DEFAULT_BFS_DEPTH, 1), MAX_BFS_DEPTH);\n\n const seenEdgeIds = new Set<string>();\n const collectedEdges: GraphEdgeRow[] = [];\n const visited = new Set<string>([`${nodeType}:${nodeId}`]);\n let frontier = new Set<string>([nodeId]);\n\n for (let hop = 0; hop < depth; hop++) {\n if (frontier.size === 0) break;\n\n const frontierArray = Array.from(frontier);\n const placeholders = frontierArray.map(() => `?`).join(', ');\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM graph_edges\n WHERE source_id IN (${placeholders}) OR target_id IN (${placeholders})`,\n ).all(...frontierArray, ...frontierArray) as Record<string, unknown>[];\n\n const nextFrontier = new Set<string>();\n\n for (const row of rows) {\n const edge = toGraphEdgeRow(row);\n if (!seenEdgeIds.has(edge.id)) {\n seenEdgeIds.add(edge.id);\n collectedEdges.push(edge);\n }\n const sourceKey = `${edge.source_type}:${edge.source_id}`;\n const targetKey = `${edge.target_type}:${edge.target_id}`;\n if (!visited.has(sourceKey)) {\n visited.add(sourceKey);\n nextFrontier.add(edge.source_id);\n }\n if (!visited.has(targetKey)) {\n visited.add(targetKey);\n nextFrontier.add(edge.target_id);\n }\n }\n\n frontier = nextFrontier;\n }\n\n return { edges: collectedEdges };\n}\n","/**\n * Lineage edge creation helpers.\n *\n * Creates automatic graph edges when spores and batches are inserted.\n * These are structural (no LLM needed) — the daemon layer calls them.\n *\n * Edge types created:\n * - FROM_SESSION: spore -> session (the session it was extracted from)\n * - EXTRACTED_FROM: spore -> batch (the prompt batch it was extracted from)\n * - DERIVED_FROM: wisdom spore -> source spore (consolidation provenance)\n * - HAS_BATCH: session -> batch (prompt batch belongs to session)\n */\n\nimport { insertGraphEdge } from './graph-edges.js';\nimport {\n EDGE_TYPE_FROM_SESSION,\n EDGE_TYPE_EXTRACTED_FROM,\n EDGE_TYPE_DERIVED_FROM,\n EDGE_TYPE_HAS_BATCH,\n} from '@myco/constants.js';\n\n// ---------------------------------------------------------------------------\n// Spore lineage\n// ---------------------------------------------------------------------------\n\n/** Create lineage edges for a newly inserted spore. */\nexport function createSporeLineage(spore: {\n id: string;\n agent_id: string;\n session_id?: string | null;\n prompt_batch_id?: number | null;\n observation_type?: string;\n properties?: string | null;\n created_at: number;\n}): void {\n if (spore.session_id) {\n insertGraphEdge({\n agent_id: spore.agent_id,\n source_id: spore.id,\n source_type: 'spore',\n target_id: spore.session_id,\n target_type: 'session',\n type: EDGE_TYPE_FROM_SESSION,\n created_at: spore.created_at,\n });\n }\n\n if (spore.prompt_batch_id != null) {\n insertGraphEdge({\n agent_id: spore.agent_id,\n source_id: spore.id,\n source_type: 'spore',\n target_id: String(spore.prompt_batch_id),\n target_type: 'batch',\n type: EDGE_TYPE_EXTRACTED_FROM,\n created_at: spore.created_at,\n });\n }\n\n // DERIVED_FROM edges for wisdom spores\n if (spore.observation_type === 'wisdom' && spore.properties) {\n try {\n const props = JSON.parse(spore.properties);\n if (Array.isArray(props.consolidated_from)) {\n for (const sourceId of props.consolidated_from) {\n insertGraphEdge({\n agent_id: spore.agent_id,\n source_id: spore.id,\n source_type: 'spore',\n target_id: sourceId,\n target_type: 'spore',\n type: EDGE_TYPE_DERIVED_FROM,\n created_at: spore.created_at,\n });\n }\n }\n } catch { /* ignore malformed properties */ }\n }\n}\n\n// ---------------------------------------------------------------------------\n// Batch lineage\n// ---------------------------------------------------------------------------\n\n/** Create a HAS_BATCH lineage edge from session to batch. */\nexport function createBatchLineage(\n agentId: string,\n sessionId: string,\n batchId: number,\n createdAt: number,\n): void {\n insertGraphEdge({\n agent_id: agentId,\n source_id: sessionId,\n source_type: 'session',\n target_id: String(batchId),\n target_type: 'batch',\n type: EDGE_TYPE_HAS_BATCH,\n created_at: createdAt,\n });\n}\n","/**\n * Entity CRUD query helpers for the knowledge graph.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { getGraphForNode, type GraphEdgeRow } from '@myco/db/queries/graph-edges.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of entities returned by listEntities when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting an entity. */\nexport interface EntityInsert {\n id: string;\n agent_id: string;\n type: string;\n name: string;\n first_seen: number;\n last_seen: number;\n properties?: string | null;\n}\n\n/** Row shape returned from entity queries (all columns). */\nexport interface EntityRow {\n id: string;\n agent_id: string;\n type: string;\n name: string;\n properties: string | null;\n first_seen: number;\n last_seen: number;\n status: string;\n}\n\n/** Filter options for `listEntities`. */\nexport interface ListEntitiesOptions {\n agent_id?: string;\n type?: string;\n /** Filter by exact entity name. */\n name?: string;\n /** Filter by status (default 'active'). */\n status?: string;\n /** Filter by entity_mentions subquery — must be paired with note_type. */\n mentioned_in?: string;\n /** Required when mentioned_in is provided. */\n note_type?: string;\n limit?: number;\n offset?: number;\n}\n\n/** Return type for `getEntityWithEdges`. */\nexport interface EntityGraph {\n center: EntityRow;\n nodes: EntityRow[];\n edges: GraphEdgeRow[];\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst ENTITY_COLUMNS = [\n 'id',\n 'agent_id',\n 'type',\n 'name',\n 'properties',\n 'first_seen',\n 'last_seen',\n 'status',\n] as const;\n\nconst SELECT_COLUMNS = ENTITY_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed EntityRow. */\nfunction toEntityRow(row: Record<string, unknown>): EntityRow {\n return {\n id: row.id as string,\n agent_id: row.agent_id as string,\n type: row.type as string,\n name: row.name as string,\n properties: (row.properties as string) ?? null,\n first_seen: row.first_seen as number,\n last_seen: row.last_seen as number,\n status: (row.status as string) ?? 'active',\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert or update an entity. Uses UPSERT on (agent_id, type, name).\n *\n * On conflict, updates properties (if provided) and last_seen.\n */\nexport function insertEntity(data: EntityInsert): EntityRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO entities (id, agent_id, type, name, properties, first_seen, last_seen)\n VALUES (?, ?, ?, ?, ?, ?, ?)\n ON CONFLICT (agent_id, type, name) DO UPDATE SET\n properties = COALESCE(EXCLUDED.properties, entities.properties),\n last_seen = EXCLUDED.last_seen`,\n ).run(\n data.id,\n data.agent_id,\n data.type,\n data.name,\n data.properties ?? null,\n data.first_seen,\n data.last_seen,\n );\n\n // On conflict, the passed-in id may not be the actual row id. Look up by unique key.\n return toEntityRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM entities WHERE agent_id = ? AND type = ? AND name = ?`).get(\n data.agent_id,\n data.type,\n data.name,\n ) as Record<string, unknown>,\n );\n}\n\n/**\n * Retrieve a single entity by id.\n *\n * @returns the entity row, or null if not found.\n */\nexport function getEntity(id: string): EntityRow | null {\n const db = getDatabase();\n\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM entities WHERE id = ?`,\n ).get(id) as Record<string, unknown> | undefined;\n\n if (!row) return null;\n return toEntityRow(row);\n}\n\n/**\n * List entities with optional filters, ordered by last_seen DESC.\n *\n * Defaults to `status = 'active'` — archived entities are excluded unless\n * `status` is explicitly provided. Pass `status: undefined` in options to\n * get only active entities (the default), or set a specific status string.\n *\n * When both `mentioned_in` and `note_type` are provided, filters to entities\n * referenced in a specific note via the entity_mentions subquery.\n */\nexport function listEntities(\n options: ListEntitiesOptions = {},\n): EntityRow[] {\n const db = getDatabase();\n\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.agent_id !== undefined) {\n conditions.push(`agent_id = ?`);\n params.push(options.agent_id);\n }\n\n if (options.type !== undefined) {\n conditions.push(`type = ?`);\n params.push(options.type);\n }\n\n if (options.name !== undefined) {\n conditions.push(`name = ?`);\n params.push(options.name);\n }\n\n // Default: only show active entities (status column added in v5)\n if (options.status !== undefined) {\n conditions.push(`status = ?`);\n params.push(options.status);\n } else {\n conditions.push(`status = ?`);\n params.push('active');\n }\n\n if (options.mentioned_in !== undefined && options.note_type !== undefined) {\n conditions.push(\n `id IN (SELECT entity_id FROM entity_mentions WHERE note_id = ? AND note_type = ?)`,\n );\n params.push(options.mentioned_in);\n params.push(options.note_type);\n }\n\n const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n const offset = options.offset ?? 0;\n\n params.push(limit);\n params.push(offset);\n\n const rows = db.prepare(\n `SELECT ${SELECT_COLUMNS}\n FROM entities\n ${where}\n ORDER BY last_seen DESC\n LIMIT ?\n OFFSET ?`,\n ).all(...params) as Record<string, unknown>[];\n\n return rows.map(toEntityRow);\n}\n\n/**\n * Fetch an entity and its surrounding graph via BFS traversal.\n *\n * Delegates to `getGraphForNode` (graph_edges table) for the BFS,\n * then fetches entity rows for all connected entity nodes.\n *\n * @param entityId - The center entity to expand from.\n * @param depth - Number of hops to traverse (1-3, default 1).\n * @returns `{ center, nodes, edges }` where nodes are all connected entities\n * (excluding center) and edges are deduplicated across BFS iterations.\n */\nexport function getEntityWithEdges(\n entityId: string,\n depth = 1,\n): EntityGraph | null {\n const db = getDatabase();\n\n const center = getEntity(entityId);\n if (center === null) return null;\n\n const clampedDepth = Math.min(Math.max(depth, 1), 3);\n const graph = getGraphForNode(entityId, 'entity', { depth: clampedDepth });\n\n // Collect all entity node IDs from edges (excluding center)\n const nodeIdSet = new Set<string>();\n for (const edge of graph.edges) {\n if (edge.source_type === 'entity' && edge.source_id !== entityId) nodeIdSet.add(edge.source_id);\n if (edge.target_type === 'entity' && edge.target_id !== entityId) nodeIdSet.add(edge.target_id);\n }\n\n // Fetch all connected entity nodes\n const nodeIds = Array.from(nodeIdSet);\n let nodes: EntityRow[] = [];\n if (nodeIds.length > 0) {\n const placeholders = nodeIds.map(() => `?`).join(', ');\n const nodeRows = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM entities WHERE id IN (${placeholders})`,\n ).all(...nodeIds) as Record<string, unknown>[];\n nodes = nodeRows.map(toEntityRow);\n }\n\n return { center, nodes, edges: graph.edges };\n}\n","/**\n * Digest extract CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { DIGEST_TIERS } from '@myco/constants.js';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required when upserting a digest extract. */\nexport interface DigestExtractUpsert {\n agent_id: string;\n tier: number;\n content: string;\n generated_at: number;\n}\n\n/** Row shape returned from digest_extracts queries (all columns). */\nexport interface DigestExtractRow {\n id: number;\n agent_id: string;\n tier: number;\n content: string;\n substrate_hash: string | null;\n generated_at: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst EXTRACT_COLUMNS = [\n 'id',\n 'agent_id',\n 'tier',\n 'content',\n 'substrate_hash',\n 'generated_at',\n] as const;\n\nconst SELECT_COLUMNS = EXTRACT_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed DigestExtractRow. */\nfunction toDigestExtractRow(row: Record<string, unknown>): DigestExtractRow {\n return {\n id: row.id as number,\n agent_id: row.agent_id as string,\n tier: row.tier as number,\n content: row.content as string,\n substrate_hash: (row.substrate_hash as string) ?? null,\n generated_at: row.generated_at as number,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Upsert a digest extract. Uses ON CONFLICT on (agent_id, tier).\n *\n * Creates or updates the extract for the given agent and token tier.\n * Uses lastInsertRowid for SERIAL PK on insert, or falls back to\n * SELECT for the conflict (update) case.\n */\nexport function upsertDigestExtract(\n data: DigestExtractUpsert,\n): DigestExtractRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO digest_extracts (agent_id, tier, content, generated_at)\n VALUES (?, ?, ?, ?)\n ON CONFLICT (agent_id, tier) DO UPDATE SET\n content = EXCLUDED.content,\n generated_at = EXCLUDED.generated_at`,\n ).run(data.agent_id, data.tier, data.content, data.generated_at);\n\n // Always look up by composite unique key — works for both insert and update cases.\n const row = db.prepare(\n `SELECT ${SELECT_COLUMNS} FROM digest_extracts WHERE agent_id = ? 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- {"version":3,"sources":["../src/hooks/client.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport { spawn } from 'node:child_process';\nimport { DAEMON_CLIENT_TIMEOUT_MS, DAEMON_HEALTH_CHECK_TIMEOUT_MS, DAEMON_HEALTH_RETRY_DELAYS, DAEMON_STALE_GRACE_PERIOD_MS } from '../constants.js';\nimport { getPluginVersion } from '../version.js';\n\ninterface DaemonInfo {\n pid: number;\n port: number;\n}\n\ninterface HealthResponse {\n myco: boolean;\n version?: string;\n}\n\ninterface ClientResult {\n ok: boolean;\n data?: any;\n}\n\nexport class DaemonClient {\n private vaultDir: string;\n\n constructor(vaultDir: string) {\n this.vaultDir = vaultDir;\n }\n\n async post(endpoint: string, body: unknown): Promise<ClientResult> {\n try {\n const info = this.readDaemonJson();\n if (!info) return { ok: false };\n\n const res = await fetch(`http://127.0.0.1:${info.port}${endpoint}`, {\n method: 'POST',\n headers: { 'Content-Type': 'application/json' },\n body: JSON.stringify(body),\n signal: AbortSignal.timeout(DAEMON_CLIENT_TIMEOUT_MS),\n });\n\n if (!res.ok) return { ok: false };\n const data = await res.json();\n return { ok: true, data };\n } catch {\n return { ok: false };\n }\n }\n\n async get(endpoint: string): Promise<ClientResult> {\n try {\n const info = this.readDaemonJson();\n if (!info) return { ok: false };\n\n const res = await fetch(`http://127.0.0.1:${info.port}${endpoint}`, {\n signal: AbortSignal.timeout(DAEMON_CLIENT_TIMEOUT_MS),\n });\n\n if (!res.ok) return { ok: false };\n const data = await res.json();\n return { ok: true, data };\n } catch {\n return { ok: false };\n }\n }\n\n async delete(endpoint: string): Promise<ClientResult> {\n try {\n const info = this.readDaemonJson();\n if (!info) return { ok: false };\n\n const res = await fetch(`http://127.0.0.1:${info.port}${endpoint}`, {\n method: 'DELETE',\n signal: AbortSignal.timeout(DAEMON_CLIENT_TIMEOUT_MS),\n });\n\n if (!res.ok) return { ok: false };\n const data = await res.json();\n return { ok: true, data };\n } catch {\n return { ok: false };\n }\n }\n\n async isHealthy(cachedInfo?: DaemonInfo | null): Promise<boolean> {\n try {\n const info = cachedInfo ?? this.readDaemonJson();\n if (!info) return false;\n\n const res = await fetch(`http://127.0.0.1:${info.port}/health`, {\n signal: AbortSignal.timeout(DAEMON_HEALTH_CHECK_TIMEOUT_MS),\n });\n if (!res.ok) return false;\n const data = await res.json() as HealthResponse;\n return data.myco === true;\n } catch {\n return false;\n }\n }\n\n /**\n * Check if the daemon is running a stale version.\n * Returns true if the daemon's version doesn't match the current plugin version.\n * Skips the check if daemon.json was written recently (grace period) to prevent\n * rapid restart loops from concurrent hooks or session reloads.\n */\n private async isStale(info: DaemonInfo): Promise<boolean> {\n try {\n const jsonPath = path.join(this.vaultDir, 'daemon.json');\n const stat = fs.statSync(jsonPath);\n if (Date.now() - stat.mtimeMs < DAEMON_STALE_GRACE_PERIOD_MS) {\n return false;\n }\n\n const res = await fetch(`http://127.0.0.1:${info.port}/health`, {\n signal: AbortSignal.timeout(DAEMON_HEALTH_CHECK_TIMEOUT_MS),\n });\n if (!res.ok) return false;\n const data = await res.json() as HealthResponse;\n if (!data.myco) return false;\n\n // No version in response = old daemon that predates this check\n if (!data.version) return true;\n\n return data.version !== getPluginVersion();\n } catch {\n return false;\n }\n }\n\n /**\n * Kill the running daemon process.\n */\n private killDaemon(info: DaemonInfo | null): void {\n try {\n if (!info) return;\n process.kill(info.pid, 'SIGTERM');\n } catch { /* already dead */ }\n try {\n fs.unlinkSync(path.join(this.vaultDir, 'daemon.json'));\n } catch { /* already gone */ }\n }\n\n /**\n * Ensure the daemon is running. 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- {"version":3,"sources":["../src/db/queries/resolution-events.ts"],"sourcesContent":["/**\n * Resolution event CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of events returned by listResolutionEvents when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a resolution event. */\nexport interface ResolutionEventInsert {\n id: string;\n agent_id: string;\n spore_id: string;\n action: string;\n created_at: number;\n new_spore_id?: string | null;\n reason?: string | null;\n session_id?: string | null;\n}\n\n/** Row shape returned from resolution_events queries (all columns). */\nexport interface ResolutionEventRow {\n id: string;\n agent_id: string;\n spore_id: string;\n action: string;\n new_spore_id: string | null;\n reason: string | null;\n session_id: string | null;\n created_at: number;\n}\n\n/** Filter options for `listResolutionEvents`. */\nexport interface ListResolutionEventsOptions {\n agent_id?: string;\n spore_id?: string;\n limit?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst EVENT_COLUMNS = [\n 'id',\n 'agent_id',\n 'spore_id',\n 'action',\n 'new_spore_id',\n 'reason',\n 'session_id',\n 'created_at',\n] as const;\n\nconst SELECT_COLUMNS = EVENT_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed ResolutionEventRow. */\nfunction toResolutionEventRow(row: Record<string, unknown>): ResolutionEventRow {\n return {\n id: row.id as string,\n agent_id: row.agent_id as string,\n spore_id: row.spore_id as string,\n action: row.action as string,\n new_spore_id: (row.new_spore_id as string) ?? null,\n reason: (row.reason as string) ?? null,\n session_id: (row.session_id as string) ?? null,\n created_at: row.created_at as number,\n };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new resolution event.\n */\nexport function insertResolutionEvent(\n data: ResolutionEventInsert,\n): ResolutionEventRow {\n const db = getDatabase();\n\n db.prepare(\n `INSERT INTO resolution_events (\n id, agent_id, spore_id, action, new_spore_id, reason, session_id, created_at\n ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,\n ).run(\n data.id,\n data.agent_id,\n data.spore_id,\n data.action,\n data.new_spore_id ?? null,\n data.reason ?? null,\n data.session_id ?? null,\n data.created_at,\n );\n\n return toResolutionEventRow(\n db.prepare(`SELECT ${SELECT_COLUMNS} FROM resolution_events WHERE id = ?`).get(data.id) as Record<string, unknown>,\n );\n}\n\n/**\n * List resolution events with optional filters, ordered by created_at DESC.\n */\nexport function listResolutionEvents(\n options: ListResolutionEventsOptions = {},\n): ResolutionEventRow[] {\n const db = getDatabase();\n\n const conditions: string[] = [];\n const params: unknown[] = [];\n\n if (options.agent_id !== undefined) {\n conditions.push(`agent_id = ?`);\n params.push(options.agent_id);\n }\n\n if (options.spore_id !== undefined) {\n conditions.push(`spore_id = ?`);\n params.push(options.spore_id);\n }\n\n const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n const limit = options.limit ?? 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