@goondocks/myco 0.6.1 → 0.6.3

package/dist/{curate-6T5NKVXK.js → curate-OHIJFBYF.js}

@@ -1,29 +1,28 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   runCuration
-} from "./chunk-2ZBB3MQT.js";
-import "./chunk-3JCXYLHD.js";
+} from "./chunk-PQWQC3RF.js";
 import {
   VectorIndex
 } from "./chunk-4RMSHZE4.js";
-import "./chunk-UVGAVYWZ.js";
-import "./chunk-24DOZEUJ.js";
+import "./chunk-ALBVNGCF.js";
 import "./chunk-RGVBGTD6.js";
 import {
   createEmbeddingProvider,
   createLlmProvider
-} from "./chunk-GDYYJTTT.js";
-import "./chunk-GNR3QAER.js";
+} from "./chunk-DBMHUMG3.js";
+import "./chunk-RY76WEN3.js";
 import "./chunk-6FQISQNA.js";
 import {
   MycoIndex
 } from "./chunk-TWSTAVLO.js";
-import "./chunk-QGJ2ZIUZ.js";
+import "./chunk-25FY74AP.js";
 import {
   loadConfig
-} from "./chunk-P3WO3N3I.js";
-import "./chunk-MQSYSQ6T.js";
-import "./chunk-6BSDCZ5Q.js";
+} from "./chunk-YG6MLLGL.js";
+import "./chunk-JSK7L46L.js";
+import "./chunk-RNWALAFP.js";
+import "./chunk-WBLTISAK.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/cli/curate.ts
@@ -77,4 +76,4 @@ Curation complete:`);
 export {
   run
 };
-//# sourceMappingURL=curate-6T5NKVXK.js.map
+//# sourceMappingURL=curate-OHIJFBYF.js.map

package/dist/{curate-6T5NKVXK.js.map → curate-OHIJFBYF.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli/curate.ts"],"sourcesContent":["/**\n * myco curate — scan the vault for stale spores and supersede them.\n *\n * Usage:\n *   myco curate              Scan and supersede stale spores\n *   myco curate --dry-run    Show what would be superseded without writing\n *\n * Algorithm:\n *   1. Load all active spores from the index\n *   2. Group by observation_type\n *   3. Within each group, embed spores and cluster by cosine similarity\n *   4. For each cluster with 2+ members, ask the LLM which are outdated\n *   5. Mark superseded: update frontmatter, append notice, re-index, remove vector\n */\nimport path from 'node:path';\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { VectorIndex } from '../index/vectors.js';\nimport { createLlmProvider, createEmbeddingProvider } from '../intelligence/llm.js';\nimport { runCuration } from '../services/vault-ops.js';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const isDryRun = args.includes('--dry-run');\n\n  const config = loadConfig(vaultDir);\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  const llmProvider = createLlmProvider(config.intelligence.llm);\n  const embeddingProvider = createEmbeddingProvider(config.intelligence.embedding);\n\n  let vectorIndex: VectorIndex | null = null;\n  try {\n    const testEmbed = await embeddingProvider.embed('test');\n    vectorIndex = new VectorIndex(path.join(vaultDir, 'vectors.db'), testEmbed.dimensions);\n  } catch (e) {\n    console.error(`Vector index unavailable: ${(e as Error).message}`);\n    console.error('Curate requires a working embedding provider.');\n    index.close();\n    process.exit(1);\n  }\n\n  try {\n    if (isDryRun) {\n      console.log('Dry run — no changes will be written.\\n');\n    }\n\n    const result = await runCuration(\n      {\n        vaultDir,\n        config,\n        index,\n        vectorIndex,\n        llmProvider,\n        embeddingProvider,\n        log: (_level, message) => console.log(`  ${message}`),\n      },\n      isDryRun,\n    );\n\n    console.log(`\\nCuration complete:`);\n    console.log(`  Scanned: ${result.scanned} active spores`);\n    console.log(`  Clusters evaluated: ${result.clustersEvaluated}`);\n    if (isDryRun) {\n      console.log(`  Would supersede: ${result.superseded}`);\n    } else {\n      console.log(`  Superseded: ${result.superseded}`);\n    }\n  } finally {\n    index.close();\n    vectorIndex?.close();\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAcA,OAAO,UAAU;AAOjB,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,WAAW,KAAK,SAAS,WAAW;AAE1C,QAAM,SAAS,WAAW,QAAQ;AAClC,QAAM,QAAQ,IAAI,UAAU,KAAK,KAAK,UAAU,UAAU,CAAC;AAE3D,QAAM,cAAc,kBAAkB,OAAO,aAAa,GAAG;AAC7D,QAAM,oBAAoB,wBAAwB,OAAO,aAAa,SAAS;AAE/E,MAAI,cAAkC;AACtC,MAAI;AACF,UAAM,YAAY,MAAM,kBAAkB,MAAM,MAAM;AACtD,kBAAc,IAAI,YAAY,KAAK,KAAK,UAAU,YAAY,GAAG,UAAU,UAAU;AAAA,EACvF,SAAS,GAAG;AACV,YAAQ,MAAM,6BAA8B,EAAY,OAAO,EAAE;AACjE,YAAQ,MAAM,+CAA+C;AAC7D,UAAM,MAAM;AACZ,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,MAAI;AACF,QAAI,UAAU;AACZ,cAAQ,IAAI,8CAAyC;AAAA,IACvD;AAEA,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,QACE;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA,KAAK,CAAC,QAAQ,YAAY,QAAQ,IAAI,KAAK,OAAO,EAAE;AAAA,MACtD;AAAA,MACA;AAAA,IACF;AAEA,YAAQ,IAAI;AAAA,mBAAsB;AAClC,YAAQ,IAAI,cAAc,OAAO,OAAO,gBAAgB;AACxD,YAAQ,IAAI,yBAAyB,OAAO,iBAAiB,EAAE;AAC/D,QAAI,UAAU;AACZ,cAAQ,IAAI,sBAAsB,OAAO,UAAU,EAAE;AAAA,IACvD,OAAO;AACL,cAAQ,IAAI,iBAAiB,OAAO,UAAU,EAAE;AAAA,IAClD;AAAA,EACF,UAAE;AACA,UAAM,MAAM;AACZ,iBAAa,MAAM;AAAA,EACrB;AACF;","names":[]}
+{"version":3,"sources":["../src/cli/curate.ts"],"sourcesContent":["/**\n * myco curate — scan the vault for stale spores and supersede them.\n *\n * Usage:\n *   myco curate              Scan and supersede stale spores\n *   myco curate --dry-run    Show what would be superseded without writing\n *\n * Algorithm:\n *   1. Load all active spores from the index\n *   2. Group by observation_type\n *   3. Within each group, embed spores and cluster by cosine similarity\n *   4. For each cluster with 2+ members, ask the LLM which are outdated\n *   5. Mark superseded: update frontmatter, append notice, re-index, remove vector\n */\nimport path from 'node:path';\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { VectorIndex } from '../index/vectors.js';\nimport { createLlmProvider, createEmbeddingProvider } from '../intelligence/llm.js';\nimport { runCuration } from '../services/vault-ops.js';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const isDryRun = args.includes('--dry-run');\n\n  const config = loadConfig(vaultDir);\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  const llmProvider = createLlmProvider(config.intelligence.llm);\n  const embeddingProvider = createEmbeddingProvider(config.intelligence.embedding);\n\n  let vectorIndex: VectorIndex | null = null;\n  try {\n    const testEmbed = await embeddingProvider.embed('test');\n    vectorIndex = new VectorIndex(path.join(vaultDir, 'vectors.db'), testEmbed.dimensions);\n  } catch (e) {\n    console.error(`Vector index unavailable: ${(e as Error).message}`);\n    console.error('Curate requires a working embedding provider.');\n    index.close();\n    process.exit(1);\n  }\n\n  try {\n    if (isDryRun) {\n      console.log('Dry run — no changes will be written.\\n');\n    }\n\n    const result = await runCuration(\n      {\n        vaultDir,\n        config,\n        index,\n        vectorIndex,\n        llmProvider,\n        embeddingProvider,\n        log: (_level, message) => console.log(`  ${message}`),\n      },\n      isDryRun,\n    );\n\n    console.log(`\\nCuration complete:`);\n    console.log(`  Scanned: ${result.scanned} active spores`);\n    console.log(`  Clusters evaluated: ${result.clustersEvaluated}`);\n    if (isDryRun) {\n      console.log(`  Would supersede: ${result.superseded}`);\n    } else {\n      console.log(`  Superseded: ${result.superseded}`);\n    }\n  } finally {\n    index.close();\n    vectorIndex?.close();\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAcA,OAAO,UAAU;AAOjB,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,WAAW,KAAK,SAAS,WAAW;AAE1C,QAAM,SAAS,WAAW,QAAQ;AAClC,QAAM,QAAQ,IAAI,UAAU,KAAK,KAAK,UAAU,UAAU,CAAC;AAE3D,QAAM,cAAc,kBAAkB,OAAO,aAAa,GAAG;AAC7D,QAAM,oBAAoB,wBAAwB,OAAO,aAAa,SAAS;AAE/E,MAAI,cAAkC;AACtC,MAAI;AACF,UAAM,YAAY,MAAM,kBAAkB,MAAM,MAAM;AACtD,kBAAc,IAAI,YAAY,KAAK,KAAK,UAAU,YAAY,GAAG,UAAU,UAAU;AAAA,EACvF,SAAS,GAAG;AACV,YAAQ,MAAM,6BAA8B,EAAY,OAAO,EAAE;AACjE,YAAQ,MAAM,+CAA+C;AAC7D,UAAM,MAAM;AACZ,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,MAAI;AACF,QAAI,UAAU;AACZ,cAAQ,IAAI,8CAAyC;AAAA,IACvD;AAEA,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,QACE;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA,KAAK,CAAC,QAAQ,YAAY,QAAQ,IAAI,KAAK,OAAO,EAAE;AAAA,MACtD;AAAA,MACA;AAAA,IACF;AAEA,YAAQ,IAAI;AAAA,mBAAsB;AAClC,YAAQ,IAAI,cAAc,OAAO,OAAO,gBAAgB;AACxD,YAAQ,IAAI,yBAAyB,OAAO,iBAAiB,EAAE;AAC/D,QAAI,UAAU;AACZ,cAAQ,IAAI,sBAAsB,OAAO,UAAU,EAAE;AAAA,IACvD,OAAO;AACL,cAAQ,IAAI,iBAAiB,OAAO,UAAU,EAAE;AAAA,IAClD;AAAA,EACF,UAAE;AACA,UAAM,MAAM;AACZ,iBAAa,MAAM;AAAA,EACrB;AACF;","names":[]}

package/dist/{detect-providers-S3M5TAMW.js → detect-providers-4U3ZPW5G.js}

@@ -2,10 +2,10 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-QGJ2ZIUZ.js";
+} from "./chunk-25FY74AP.js";
 import {
   PROVIDER_DETECT_TIMEOUT_MS
-} from "./chunk-6BSDCZ5Q.js";
+} from "./chunk-WBLTISAK.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/cli/detect-providers.ts
@@ -32,4 +32,4 @@ async function run(_args) {
 export {
   run
 };
-//# sourceMappingURL=detect-providers-S3M5TAMW.js.map
+//# sourceMappingURL=detect-providers-4U3ZPW5G.js.map

package/dist/{digest-O35VHYFP.js → digest-I2XYCK2M.js}

@@ -1,30 +1,28 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   runDigest
-} from "./chunk-2ZBB3MQT.js";
-import "./chunk-3JCXYLHD.js";
-import "./chunk-UVGAVYWZ.js";
-import "./chunk-24DOZEUJ.js";
+} from "./chunk-PQWQC3RF.js";
+import "./chunk-ALBVNGCF.js";
 import "./chunk-RGVBGTD6.js";
 import {
   createLlmProvider
-} from "./chunk-GDYYJTTT.js";
-import "./chunk-GNR3QAER.js";
+} from "./chunk-DBMHUMG3.js";
+import "./chunk-RY76WEN3.js";
 import "./chunk-6FQISQNA.js";
 import {
   MycoIndex
 } from "./chunk-TWSTAVLO.js";
-import "./chunk-2YBUL3IL.js";
+import "./chunk-4WL5X7VS.js";
 import {
   parseIntFlag
 } from "./chunk-SAKJMNSR.js";
-import "./chunk-QGJ2ZIUZ.js";
+import "./chunk-25FY74AP.js";
 import {
   loadConfig
-} from "./chunk-P3WO3N3I.js";
-import "./chunk-MQSYSQ6T.js";
-import "./chunk-5QWZT4AB.js";
-import "./chunk-6BSDCZ5Q.js";
+} from "./chunk-YG6MLLGL.js";
+import "./chunk-JSK7L46L.js";
+import "./chunk-RNWALAFP.js";
+import "./chunk-WBLTISAK.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/cli/digest.ts
@@ -84,4 +82,4 @@ Digest cycle complete:`);
 export {
   run
 };
-//# sourceMappingURL=digest-O35VHYFP.js.map
+//# sourceMappingURL=digest-I2XYCK2M.js.map

package/dist/{digest-O35VHYFP.js.map → digest-I2XYCK2M.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli/digest.ts"],"sourcesContent":["/**\n * myco digest — run a digest cycle from the CLI.\n *\n * Usage:\n *   myco digest              Incremental cycle (only new substrate)\n *   myco digest --full       Full reprocess of all tiers from clean slate\n *   myco digest --tier 3000  Reprocess a specific tier from clean slate\n *\n * When --tier or --full is used, the cycle processes ALL vault notes (not just\n * new ones) and ignores previous extracts, producing a clean synthesis.\n */\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { createLlmProvider } from '../intelligence/llm.js';\nimport { runDigest } from '../services/vault-ops.js';\nimport { parseIntFlag } from './shared.js';\nimport path from 'node:path';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const config = loadConfig(vaultDir);\n\n  if (!config.digest.enabled) {\n    console.error('Digest is not enabled. Set digest.enabled: true in myco.yaml.');\n    process.exit(1);\n  }\n\n  const tierArg = parseIntFlag(args, '--tier');\n  const isFull = args.includes('--full');\n  const isReprocess = isFull || tierArg !== undefined;\n\n  // Resolve the digest LLM provider\n  const digestLlmConfig = {\n    provider: config.digest.intelligence.provider ?? config.intelligence.llm.provider,\n    model: config.digest.intelligence.model ?? config.intelligence.llm.model,\n    base_url: config.digest.intelligence.base_url ?? config.intelligence.llm.base_url,\n    context_window: config.digest.intelligence.context_window,\n  };\n  const llmProvider = createLlmProvider(digestLlmConfig);\n\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  if (isReprocess) {\n    const tierLabel = tierArg ? `tier ${tierArg}` : 'all tiers';\n    console.log(`Full reprocess of ${tierLabel} — clean slate, all substrate`);\n  } else {\n    console.log('Running incremental digest cycle');\n  }\n\n  try {\n    const result = await runDigest(\n      {\n        vaultDir,\n        config,\n        index,\n        log: (level, message, data) => {\n          const prefix = level === 'warn' ? '!' : level === 'info' ? '>' : '  ';\n          const suffix = data ? ` ${JSON.stringify(data)}` : '';\n          console.log(`${prefix} ${message}${suffix}`);\n        },\n      },\n      llmProvider,\n      { tier: tierArg, full: isFull },\n    );\n\n    if (!result) {\n      console.log('No substrate found — nothing to digest.');\n      return;\n    }\n\n    console.log(`\\nDigest cycle complete:`);\n    console.log(`  Tiers generated: [${result.tiersGenerated.join(', ')}]`);\n    console.log(`  Substrate: ${Object.values(result.substrate).flat().length} notes`);\n    console.log(`  Duration: ${(result.durationMs / 1000).toFixed(1)}s`);\n    console.log(`  Model: ${result.model}`);\n  } finally {\n    index.close();\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAgBA,OAAO,UAAU;AAEjB,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,SAAS,WAAW,QAAQ;AAElC,MAAI,CAAC,OAAO,OAAO,SAAS;AAC1B,YAAQ,MAAM,+DAA+D;AAC7E,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,QAAM,UAAU,aAAa,MAAM,QAAQ;AAC3C,QAAM,SAAS,KAAK,SAAS,QAAQ;AACrC,QAAM,cAAc,UAAU,YAAY;AAG1C,QAAM,kBAAkB;AAAA,IACtB,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,OAAO,OAAO,OAAO,aAAa,SAAS,OAAO,aAAa,IAAI;AAAA,IACnE,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,gBAAgB,OAAO,OAAO,aAAa;AAAA,EAC7C;AACA,QAAM,cAAc,kBAAkB,eAAe;AAErD,QAAM,QAAQ,IAAI,UAAU,KAAK,KAAK,UAAU,UAAU,CAAC;AAE3D,MAAI,aAAa;AACf,UAAM,YAAY,UAAU,QAAQ,OAAO,KAAK;AAChD,YAAQ,IAAI,qBAAqB,SAAS,oCAA+B;AAAA,EAC3E,OAAO;AACL,YAAQ,IAAI,kCAAkC;AAAA,EAChD;AAEA,MAAI;AACF,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,QACE;AAAA,QACA;AAAA,QACA;AAAA,QACA,KAAK,CAAC,OAAO,SAAS,SAAS;AAC7B,gBAAM,SAAS,UAAU,SAAS,MAAM,UAAU,SAAS,MAAM;AACjE,gBAAM,SAAS,OAAO,IAAI,KAAK,UAAU,IAAI,CAAC,KAAK;AACnD,kBAAQ,IAAI,GAAG,MAAM,IAAI,OAAO,GAAG,MAAM,EAAE;AAAA,QAC7C;AAAA,MACF;AAAA,MACA;AAAA,MACA,EAAE,MAAM,SAAS,MAAM,OAAO;AAAA,IAChC;AAEA,QAAI,CAAC,QAAQ;AACX,cAAQ,IAAI,8CAAyC;AACrD;AAAA,IACF;AAEA,YAAQ,IAAI;AAAA,uBAA0B;AACtC,YAAQ,IAAI,uBAAuB,OAAO,eAAe,KAAK,IAAI,CAAC,GAAG;AACtE,YAAQ,IAAI,gBAAgB,OAAO,OAAO,OAAO,SAAS,EAAE,KAAK,EAAE,MAAM,QAAQ;AACjF,YAAQ,IAAI,gBAAgB,OAAO,aAAa,KAAM,QAAQ,CAAC,CAAC,GAAG;AACnE,YAAQ,IAAI,YAAY,OAAO,KAAK,EAAE;AAAA,EACxC,UAAE;AACA,UAAM,MAAM;AAAA,EACd;AACF;","names":[]}
+{"version":3,"sources":["../src/cli/digest.ts"],"sourcesContent":["/**\n * myco digest — run a digest cycle from the CLI.\n *\n * Usage:\n *   myco digest              Incremental cycle (only new substrate)\n *   myco digest --full       Full reprocess of all tiers from clean slate\n *   myco digest --tier 3000  Reprocess a specific tier from clean slate\n *\n * When --tier or --full is used, the cycle processes ALL vault notes (not just\n * new ones) and ignores previous extracts, producing a clean synthesis.\n */\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { createLlmProvider } from '../intelligence/llm.js';\nimport { runDigest } from '../services/vault-ops.js';\nimport { parseIntFlag } from './shared.js';\nimport path from 'node:path';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const config = loadConfig(vaultDir);\n\n  if (!config.digest.enabled) {\n    console.error('Digest is not enabled. Set digest.enabled: true in myco.yaml.');\n    process.exit(1);\n  }\n\n  const tierArg = parseIntFlag(args, '--tier');\n  const isFull = args.includes('--full');\n  const isReprocess = isFull || tierArg !== undefined;\n\n  // Resolve the digest LLM provider\n  const digestLlmConfig = {\n    provider: config.digest.intelligence.provider ?? config.intelligence.llm.provider,\n    model: config.digest.intelligence.model ?? config.intelligence.llm.model,\n    base_url: config.digest.intelligence.base_url ?? config.intelligence.llm.base_url,\n    context_window: config.digest.intelligence.context_window,\n  };\n  const llmProvider = createLlmProvider(digestLlmConfig);\n\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  if (isReprocess) {\n    const tierLabel = tierArg ? `tier ${tierArg}` : 'all tiers';\n    console.log(`Full reprocess of ${tierLabel} — clean slate, all substrate`);\n  } else {\n    console.log('Running incremental digest cycle');\n  }\n\n  try {\n    const result = await runDigest(\n      {\n        vaultDir,\n        config,\n        index,\n        log: (level, message, data) => {\n          const prefix = level === 'warn' ? '!' : level === 'info' ? '>' : '  ';\n          const suffix = data ? ` ${JSON.stringify(data)}` : '';\n          console.log(`${prefix} ${message}${suffix}`);\n        },\n      },\n      llmProvider,\n      { tier: tierArg, full: isFull },\n    );\n\n    if (!result) {\n      console.log('No substrate found — nothing to digest.');\n      return;\n    }\n\n    console.log(`\\nDigest cycle complete:`);\n    console.log(`  Tiers generated: [${result.tiersGenerated.join(', ')}]`);\n    console.log(`  Substrate: ${Object.values(result.substrate).flat().length} notes`);\n    console.log(`  Duration: ${(result.durationMs / 1000).toFixed(1)}s`);\n    console.log(`  Model: ${result.model}`);\n  } finally {\n    index.close();\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAgBA,OAAO,UAAU;AAEjB,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,SAAS,WAAW,QAAQ;AAElC,MAAI,CAAC,OAAO,OAAO,SAAS;AAC1B,YAAQ,MAAM,+DAA+D;AAC7E,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,QAAM,UAAU,aAAa,MAAM,QAAQ;AAC3C,QAAM,SAAS,KAAK,SAAS,QAAQ;AACrC,QAAM,cAAc,UAAU,YAAY;AAG1C,QAAM,kBAAkB;AAAA,IACtB,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,OAAO,OAAO,OAAO,aAAa,SAAS,OAAO,aAAa,IAAI;AAAA,IACnE,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,gBAAgB,OAAO,OAAO,aAAa;AAAA,EAC7C;AACA,QAAM,cAAc,kBAAkB,eAAe;AAErD,QAAM,QAAQ,IAAI,UAAU,KAAK,KAAK,UAAU,UAAU,CAAC;AAE3D,MAAI,aAAa;AACf,UAAM,YAAY,UAAU,QAAQ,OAAO,KAAK;AAChD,YAAQ,IAAI,qBAAqB,SAAS,oCAA+B;AAAA,EAC3E,OAAO;AACL,YAAQ,IAAI,kCAAkC;AAAA,EAChD;AAEA,MAAI;AACF,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,QACE;AAAA,QACA;AAAA,QACA;AAAA,QACA,KAAK,CAAC,OAAO,SAAS,SAAS;AAC7B,gBAAM,SAAS,UAAU,SAAS,MAAM,UAAU,SAAS,MAAM;AACjE,gBAAM,SAAS,OAAO,IAAI,KAAK,UAAU,IAAI,CAAC,KAAK;AACnD,kBAAQ,IAAI,GAAG,MAAM,IAAI,OAAO,GAAG,MAAM,EAAE;AAAA,QAC7C;AAAA,MACF;AAAA,MACA;AAAA,MACA,EAAE,MAAM,SAAS,MAAM,OAAO;AAAA,IAChC;AAEA,QAAI,CAAC,QAAQ;AACX,cAAQ,IAAI,8CAAyC;AACrD;AAAA,IACF;AAEA,YAAQ,IAAI;AAAA,uBAA0B;AACtC,YAAQ,IAAI,uBAAuB,OAAO,eAAe,KAAK,IAAI,CAAC,GAAG;AACtE,YAAQ,IAAI,gBAAgB,OAAO,OAAO,OAAO,SAAS,EAAE,KAAK,EAAE,MAAM,QAAQ;AACjF,YAAQ,IAAI,gBAAgB,OAAO,aAAa,KAAM,QAAQ,CAAC,CAAC,GAAG;AACnE,YAAQ,IAAI,YAAY,OAAO,KAAK,EAAE;AAAA,EACxC,UAAE;AACA,UAAM,MAAM;AAAA,EACd;AACF;","names":[]}

package/dist/{init-TFLSATB3.js → init-ZO2XQT6U.js}

@@ -7,27 +7,27 @@ import {
 } from "./chunk-TWSTAVLO.js";
 import {
   run
-} from "./chunk-5FNZ7AMX.js";
+} from "./chunk-IWBWZQK6.js";
 import {
   run as run2
-} from "./chunk-YTANWAGE.js";
+} from "./chunk-XNAM6Z4O.js";
 import {
   VAULT_GITIGNORE,
   configureVaultEnv
-} from "./chunk-2YBUL3IL.js";
+} from "./chunk-4WL5X7VS.js";
 import {
   parseStringFlag
 } from "./chunk-SAKJMNSR.js";
-import "./chunk-QGJ2ZIUZ.js";
+import "./chunk-25FY74AP.js";
 import {
   MycoConfigSchema,
   require_dist
-} from "./chunk-MQSYSQ6T.js";
+} from "./chunk-JSK7L46L.js";
 import {
   resolveVaultDir
 } from "./chunk-N33KUCFP.js";
-import "./chunk-5QWZT4AB.js";
-import "./chunk-6BSDCZ5Q.js";
+import "./chunk-RNWALAFP.js";
+import "./chunk-WBLTISAK.js";
 import {
   __toESM
 } from "./chunk-PZUWP5VK.js";
@@ -106,4 +106,4 @@ async function run3(args) {
 export {
   run3 as run
 };
-//# sourceMappingURL=init-TFLSATB3.js.map
+//# sourceMappingURL=init-ZO2XQT6U.js.map

package/dist/{main-JEUQS3BY.js → main-XZ6X4BUX.js}

@@ -1,35 +1,26 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
-import {
-  BufferProcessor,
-  TranscriptMiner,
-  extractTurnsFromBuffer,
-  writeObservationNotes
-} from "./chunk-B5UZSHQV.js";
 import {
   gatherStats
-} from "./chunk-ZMYNRTTD.js";
+} from "./chunk-WU4PCNIK.js";
 import {
+  BufferProcessor,
   DigestEngine,
   Metabolism,
+  SUMMARIZATION_FAILED_MARKER,
+  TranscriptMiner,
   appendTraceRecord,
+  extractTurnsFromBuffer,
   readLastTimestamp,
   runCuration,
   runDigest,
-  runRebuild
-} from "./chunk-2ZBB3MQT.js";
-import "./chunk-3JCXYLHD.js";
+  runRebuild,
+  runReprocess,
+  writeObservationNotes
+} from "./chunk-PQWQC3RF.js";
 import {
   consolidateSpores,
   handleMycoContext
-} from "./chunk-KUMVJIJW.js";
-import {
-  VaultWriter,
-  bareSessionId,
-  formatSessionBody,
-  sessionNoteId,
-  sessionRelativePath,
-  sessionWikilink
-} from "./chunk-KC7ENQTN.js";
+} from "./chunk-LDKXXKF6.js";
 import {
   DaemonLogger
 } from "./chunk-QLUE3BUL.js";
@@ -37,59 +28,65 @@ import {
   VectorIndex
 } from "./chunk-4RMSHZE4.js";
 import {
-  checkSupersession,
-  isActiveSpore
-} from "./chunk-UVGAVYWZ.js";
-import {
+  CONVERSATION_HEADING,
+  VaultWriter,
+  bareSessionId,
   buildSimilarityPrompt,
+  checkSupersession,
+  extractJson,
   extractNumber,
   formatNotesForPrompt,
+  formatSessionBody,
   indexNote,
+  isActiveSpore,
   loadPrompt,
   rebuildIndex,
+  sessionNoteId,
+  sessionRelativePath,
+  sessionWikilink,
   stripReasoningTokens
-} from "./chunk-24DOZEUJ.js";
+} from "./chunk-ALBVNGCF.js";
 import {
   generateEmbedding
 } from "./chunk-RGVBGTD6.js";
 import {
   createEmbeddingProvider,
   createLlmProvider
-} from "./chunk-GDYYJTTT.js";
-import "./chunk-GNR3QAER.js";
+} from "./chunk-DBMHUMG3.js";
+import "./chunk-RY76WEN3.js";
 import {
   initFts
 } from "./chunk-6FQISQNA.js";
 import {
   MycoIndex
 } from "./chunk-TWSTAVLO.js";
-import "./chunk-2YBUL3IL.js";
+import "./chunk-4WL5X7VS.js";
 import "./chunk-SAKJMNSR.js";
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-QGJ2ZIUZ.js";
+} from "./chunk-25FY74AP.js";
 import {
   CONFIG_FILENAME,
   loadConfig,
   saveConfig
-} from "./chunk-P3WO3N3I.js";
+} from "./chunk-YG6MLLGL.js";
 import {
   MycoConfigSchema,
   external_exports,
   require_dist
-} from "./chunk-MQSYSQ6T.js";
+} from "./chunk-JSK7L46L.js";
 import {
   EventBuffer
 } from "./chunk-HIN3UVOG.js";
 import {
   getPluginVersion
-} from "./chunk-E7OBRBCQ.js";
+} from "./chunk-CK24O5YQ.js";
 import {
   claudeCodeAdapter,
   createPerProjectAdapter,
   extensionForMimeType
-} from "./chunk-5QWZT4AB.js";
+} from "./chunk-RNWALAFP.js";
 import {
   CANDIDATE_CONTENT_PREVIEW,
   CONSOLIDATION_MAX_TOKENS,
@@ -97,6 +94,8 @@ import {
   CONSOLIDATION_VECTOR_FETCH_LIMIT,
   CONTENT_SNIPPET_CHARS,
   CONTEXT_SESSION_PREVIEW_CHARS,
+  DAEMON_EVICT_POLL_MS,
+  DAEMON_EVICT_TIMEOUT_MS,
   EMBEDDING_INPUT_LIMIT,
   FILE_WATCH_STABILITY_MS,
   LINEAGE_RECENT_SESSIONS_LIMIT,
@@ -108,7 +107,7 @@ import {
   RELATED_SPORES_LIMIT,
   SESSION_CONTEXT_MAX_PLANS,
   STALE_BUFFER_MAX_AGE_MS
-} from "./chunk-6BSDCZ5Q.js";
+} from "./chunk-WBLTISAK.js";
 import {
   __toESM
 } from "./chunk-PZUWP5VK.js";
@@ -322,6 +321,57 @@ var DaemonServer = class {
     } catch {
     }
   }
+  /**
+   * Kill any existing daemon for this vault before taking over.
+   * Prevents orphaned daemons when spawned from worktrees or plugin upgrades.
+   * Must be called BEFORE resolvePort() so the old daemon releases the port.
+   */
+  async evictExistingDaemon() {
+    const jsonPath = path2.join(this.vaultDir, "daemon.json");
+    let existingPid;
+    try {
+      const content = fs2.readFileSync(jsonPath, "utf-8");
+      const info = JSON.parse(content);
+      if (typeof info.pid === "number" && info.pid !== process.pid) {
+        existingPid = info.pid;
+      }
+    } catch {
+    }
+    if (!existingPid) return;
+    try {
+      process.kill(existingPid, 0);
+    } catch {
+      return;
+    }
+    this.logger.info("daemon", "Evicting existing daemon", { pid: existingPid });
+    try {
+      process.kill(existingPid, "SIGTERM");
+    } catch {
+      return;
+    }
+    const deadline = Date.now() + DAEMON_EVICT_TIMEOUT_MS;
+    while (Date.now() < deadline) {
+      await new Promise((r) => setTimeout(r, DAEMON_EVICT_POLL_MS));
+      try {
+        process.kill(existingPid, 0);
+      } catch {
+        return;
+      }
+    }
+    this.logger.warn("daemon", "Evicted daemon did not exit in time, sending SIGKILL", { pid: existingPid });
+    try {
+      process.kill(existingPid, "SIGKILL");
+    } catch {
+      return;
+    }
+    await new Promise((r) => setTimeout(r, DAEMON_EVICT_POLL_MS));
+    try {
+      process.kill(existingPid, 0);
+    } catch {
+      return;
+    }
+    this.logger.warn("daemon", "Evicted daemon still alive after SIGKILL", { pid: existingPid });
+  }
   writeDaemonJson() {
     const info = {
       pid: process.pid,
@@ -335,6 +385,9 @@ var DaemonServer = class {
   removeDaemonJson() {
     const jsonPath = path2.join(this.vaultDir, "daemon.json");
     try {
+      const content = fs2.readFileSync(jsonPath, "utf-8");
+      const info = JSON.parse(content);
+      if (info.pid !== process.pid) return;
       fs2.unlinkSync(jsonPath);
     } catch {
     }
@@ -2368,6 +2421,7 @@ var consolidationResponseSchema = external_exports.discriminatedUnion("consolida
 var CONSOLIDATION_TRACE_FILENAME = "consolidation-trace.jsonl";
 var ConsolidationEngine = class {
   deps;
+  maxTokens;
   log;
   lastTimestampCache = void 0;
   constructor(config) {
@@ -2378,6 +2432,7 @@ var ConsolidationEngine = class {
       llmProvider: config.llmProvider,
       embeddingProvider: config.embeddingProvider
     };
+    this.maxTokens = config.maxTokens ?? CONSOLIDATION_MAX_TOKENS;
     this.log = config.log ?? (() => {
     });
   }
@@ -2492,11 +2547,11 @@ var ConsolidationEngine = class {
       }
       clustersFound++;
       const candidatesText = formatNotesForPrompt(cluster);
-      const prompt = template.replace("{{count}}", String(cluster.length)).replace("{{observation_type}}", observationType ?? "unknown").replace("{{candidates}}", candidatesText);
+      const prompt = template.replace("{{count}}", String(cluster.length)).replace("{{observation_type}}", observationType ?? "unknown").replace("{{candidates}}", candidatesText).replace("{{maxTokens}}", String(this.maxTokens));
       let responseText;
       try {
         const response = await llmProvider.summarize(prompt, {
-          maxTokens: CONSOLIDATION_MAX_TOKENS,
+          maxTokens: this.maxTokens,
           reasoning: LLM_REASONING_MODE
         });
         responseText = stripReasoningTokens(response.text);
@@ -2510,7 +2565,7 @@ var ConsolidationEngine = class {
       }
       let parsed;
       try {
-        const raw = JSON.parse(responseText);
+        const raw = extractJson(responseText);
         const result = consolidationResponseSchema.safeParse(raw);
         if (!result.success) {
           this.log("warn", "ConsolidationEngine: LLM response failed schema validation", {
@@ -2737,7 +2792,7 @@ async function handleGetStats(deps) {
   const digestConfig = deps.config.digest;
   const digest = {
     enabled: digestConfig.enabled,
-    consolidation_enabled: digestConfig.consolidation,
+    consolidation_enabled: digestConfig.consolidation.enabled,
     metabolism_state: deps.metabolism?.state ?? null,
     last_cycle: null,
     substrate_queue: 0
@@ -2925,6 +2980,12 @@ var DigestBody = external_exports.object({
   tier: external_exports.number().int().positive().optional(),
   full: external_exports.boolean().optional()
 }).optional();
+var ReprocessBody = external_exports.object({
+  session: external_exports.string().optional(),
+  date: external_exports.string().optional(),
+  failed: external_exports.boolean().optional(),
+  index_only: external_exports.boolean().optional()
+}).optional();
 async function handleRebuild(deps) {
   const { token, isNew } = deps.progressTracker.create("rebuild");
   if (!isNew) {
@@ -3062,6 +3123,56 @@ async function handleCurate(deps, body, runCuration2) {
   });
   return { body: { token } };
 }
+async function handleReprocess(deps, body) {
+  const parsed = ReprocessBody.safeParse(body);
+  if (!parsed.success) {
+    return { status: 400, body: { error: "validation_failed", issues: parsed.error.issues } };
+  }
+  const options = {
+    session: parsed.data?.session,
+    date: parsed.data?.date,
+    failed: parsed.data?.failed,
+    indexOnly: parsed.data?.index_only
+  };
+  const { token, isNew } = deps.progressTracker.create("reprocess");
+  if (!isNew) {
+    return { body: { token, status: "already_running" } };
+  }
+  runReprocess(
+    {
+      vaultDir: deps.vaultDir,
+      config: deps.config,
+      index: deps.index,
+      vectorIndex: deps.vectorIndex ?? void 0,
+      log: deps.log
+    },
+    deps.llmProvider,
+    deps.embeddingProvider,
+    options,
+    (phase, done, total) => {
+      const percent = total > 0 ? Math.round(done / total * PROGRESS_COMPLETE) : 0;
+      deps.progressTracker.update(token, {
+        percent,
+        message: `${phase}: ${done}/${total}`
+      });
+    }
+  ).then((result) => {
+    const message = result.sessionsProcessed === 0 ? `No matching sessions found (${result.sessionsFound} checked)` : `${result.sessionsProcessed} sessions, ${result.observationsExtracted} observations, ${result.summariesRegenerated} summaries`;
+    deps.progressTracker.update(token, {
+      status: "completed",
+      percent: PROGRESS_COMPLETE,
+      message
+    });
+    deps.log("info", "Reprocess completed via API", { ...result });
+  }).catch((err) => {
+    deps.progressTracker.update(token, {
+      status: "failed",
+      message: err.message
+    });
+    deps.log("warn", "Reprocess failed via API", { error: err.message });
+  });
+  return { body: { token } };
+}
 
 // src/daemon/api/models.ts
 var MODEL_LIST_TIMEOUT_MS = 5e3;
@@ -3117,6 +3228,28 @@ async function handleGetModels(req) {
   return { body: { provider, models } };
 }
 
+// src/daemon/api/sessions.ts
+function handleGetSessions(index) {
+  const notes = index.query({ type: "session" });
+  const dateSet = /* @__PURE__ */ new Set();
+  const sessions = [];
+  for (const note of notes) {
+    const parts = note.path.split("/");
+    const date = parts[1] ?? "";
+    const filename = parts[2] ?? "";
+    const id = filename.replace("session-", "").replace(".md", "");
+    dateSet.add(date);
+    sessions.push({
+      id,
+      date,
+      title: note.title || id.slice(0, 8),
+      hasFailed: note.content.includes(SUMMARIZATION_FAILED_MARKER)
+    });
+  }
+  const dates = [...dateSet].sort().reverse();
+  return { body: { sessions, dates } };
+}
+
 // src/daemon/main.ts
 var import_yaml = __toESM(require_dist(), 1);
 import fs6 from "fs";
@@ -3371,13 +3504,14 @@ ${content}`,
       config,
       log: (level, message, data) => logger[level]("digest", message, data)
     });
-    if (config.digest.consolidation) {
+    if (config.digest.consolidation.enabled) {
       const consolidationEngine = new ConsolidationEngine({
         vaultDir,
         index,
         vectorIndex,
         embeddingProvider,
         llmProvider: digestLlm,
+        maxTokens: config.digest.consolidation.max_tokens,
         log: (level, message, data) => logger[level]("consolidation", message, data)
       });
       digestEngine.registerPrePass("consolidation", async () => {
@@ -3639,7 +3773,7 @@ ${content}`,
       if (t.aiResponse) parts.push(`Response: ${t.aiResponse}`);
       return parts.join("\n");
     }).join("\n\n");
-    const conversationSection = `## Conversation
+    const conversationSection = `${CONVERSATION_HEADING}
 
 ${conversationText}`;
     const observationPromise = lastBatch.length > 0 ? processor.process(lastBatch, sessionId).catch((err) => {
@@ -3921,6 +4055,9 @@ ${lines.join("\n")}`;
   server.registerRoute("POST", "/api/rebuild", async () => handleRebuild(operationDeps));
   server.registerRoute("POST", "/api/digest", async (req) => handleDigest(operationDeps, req.body));
   server.registerRoute("POST", "/api/curate", async (req) => handleCurate(operationDeps, req.body, runCuration));
+  server.registerRoute("POST", "/api/reprocess", async (req) => handleReprocess(operationDeps, req.body));
+  server.registerRoute("GET", "/api/sessions", async () => handleGetSessions(index));
+  await server.evictExistingDaemon();
   const resolvedPort = await resolvePort(config.daemon.port, vaultDir);
   if (resolvedPort === 0) {
     logger.warn("daemon", "All preferred ports occupied, using ephemeral port");
@@ -3977,4 +4114,4 @@ export {
 chokidar/index.js:
   (*! chokidar - MIT License (c) 2012 Paul Miller (paulmillr.com) *)
 */
-//# sourceMappingURL=main-JEUQS3BY.js.map
+//# sourceMappingURL=main-XZ6X4BUX.js.map