@knowledgine/cli 0.6.1 → 0.6.3

package/dist/index.js

@@ -20,6 +20,8 @@ import { registerFeedbackSuggestCommand } from "./commands/feedback-suggest.js";
 import { registerServeCommand } from "./commands/serve.js";
 import { deprecationCheckCommand } from "./commands/deprecation-check.js";
 import { undeprecateCommand } from "./commands/undeprecate.js";
+import { doctorCommand } from "./commands/doctor.js";
+import { benchmarkCommand } from "./commands/benchmark.js";
 import { createOutputErrorHandler } from "./lib/unknown-command-handler.js";
 const program = new Command();
 program
@@ -27,13 +29,16 @@ program
     .description("Developer Knowledge Infrastructure - Extract structured knowledge from your codebase")
     .version(`v${VERSION} (node ${process.version})`)
     .addHelpText("after", `
-Workflow:
-  1. knowledgine init --path ~/notes    Index your files (FTS5 full-text search)
-  2. knowledgine setup --target claude-desktop  Configure AI tool
-  3. knowledgine start --path ~/notes    Start MCP server
+Quick Start:
+  1. knowledgine init --path .          Index your files
+  2. knowledgine ingest --all --path .  Ingest from all sources
+  3. knowledgine search "query"         Search your knowledge base
 
-Optional:
-  knowledgine upgrade --semantic         Enable semantic search (downloads ~23MB model)
+MCP Integration:
+  1. knowledgine init --path .
+  2. knowledgine ingest --all --path .
+  3. knowledgine setup --target claude-code
+  4. knowledgine start --path .
 
 Run 'knowledgine <command> --help' for more information on a command.`);
 program
@@ -91,14 +96,22 @@ program
 Example:
   knowledgine status --path ~/notes`)
     .action(statusCommand);
+// Top-level stats alias (shortcut for tool stats)
+program
+    .command("stats")
+    .description("Show knowledge base statistics (alias for status)")
+    .option("--path <dir>", "Root directory to check")
+    .action(statusCommand);
 program
     .command("upgrade")
     .description("Upgrade knowledgine capabilities")
     .option("--semantic", "Enable semantic search (download model + generate embeddings)")
+    .option("--reindex", "Delete and regenerate all embeddings (use after switching embedding models)")
     .option("--path <dir>", "Root directory")
     .addHelpText("after", `
-Example:
-  knowledgine upgrade --semantic --path ~/notes`)
+Examples:
+  knowledgine upgrade --semantic --path ~/notes
+  knowledgine upgrade --reindex`)
     .action(upgradeCommand);
 program
     .command("ingest")
@@ -119,6 +132,7 @@ program
     .option("--observe", "Run Observer/Reflector agents after ingestion")
     .option("--no-observe", "Skip Observer/Reflector agents")
     .option("--observe-limit <n>", "Max notes to process with Observer", parseInt)
+    .option("--no-embeddings", "Skip embedding generation after ingest (semantic search will not work for these notes)")
     .addHelpText("after", `
 Examples:
   knowledgine ingest --source markdown --path ~/notes
@@ -191,10 +205,11 @@ program
     .command("search <query>")
     .description("Search indexed notes")
     .option("--demo", "Search in demo notes")
-    .option("--mode <mode>", "Search mode: keyword, semantic, hybrid", "keyword")
+    .option("--mode <mode>", "Search mode: keyword, semantic, hybrid (default: auto-detect)")
     .option("--limit <n>", "Maximum results", "20")
     .option("--format <format>", "Output format: json, table, plain", "plain")
-    .option("--related <noteId>", "Find related notes by note ID")
+    .option("--related", "Find related notes (uses query as note ID or entity name)")
+    .option("--related-entity <name>", "Explicitly specify entity name for related search")
     .option("--related-file <path>", "Find related notes by file path")
     .option("--path <dir>", "Root directory")
     .option("--no-fallback", "Exit with error if requested search mode is unavailable (instead of falling back to keyword)")
@@ -208,6 +223,7 @@ program
         limit: Number(opts.limit),
         format: opts.format,
         related: opts.related,
+        relatedEntity: opts.relatedEntity,
         relatedFile: opts.relatedFile,
         path: opts.path,
         fallback: opts.fallback,
@@ -250,12 +266,31 @@ program
     .option("--path <dir>", "Root directory")
     .option("--apply", "Apply deprecation (default: dry-run)")
     .option("--threshold <n>", "Similarity threshold (0-1, default: 0.8)", "0.8")
+    .option("--exclude-translations", "Exclude translation files (.po, .xlf) from comparison")
     .action(deprecationCheckCommand);
 program
     .command("undeprecate <noteId>")
     .description("Restore a deprecated note to active status")
     .option("--path <dir>", "Root directory")
     .action(undeprecateCommand);
+program
+    .command("doctor")
+    .description("Run comprehensive health checks on your knowledge base")
+    .option("--path <dir>", "Root directory to check")
+    .option("--fix", "Automatically fix issues where possible")
+    .addHelpText("after", `
+Example:
+  knowledgine doctor --path ~/notes`)
+    .action(doctorCommand);
+program
+    .command("benchmark")
+    .description("Run benchmarks on the knowledge base")
+    .option("--path <dir>", "Root directory")
+    .option("--semantic", "Analyze semantic score distribution (requires embeddings)")
+    .addHelpText("after", `
+Example:
+  knowledgine benchmark --semantic --path ~/notes`)
+    .action(benchmarkCommand);
 program.showSuggestionAfterError(true);
 program.configureOutput({
     outputError: createOutputErrorHandler(() => program.commands.map((c) => c.name())),

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/lib/entity-extractor.d.ts

@@ -0,0 +1,17 @@
+import { KnowledgeRepository, GraphRepository } from "@knowledgine/core";
+export interface PostIngestSummary {
+    totalNotes: number;
+    processedNotes: number;
+    totalEntities: number;
+    totalRelations: number;
+    totalPatterns: number;
+    errors: number;
+}
+/**
+ * 全ノートに対してパターン抽出、エンティティ抽出、関係推論をバッチ実行する。
+ * init コマンドから ingest パイプライン経由でノートが保存された後に呼ばれる。
+ *
+ * @deprecated 新規コードは IncrementalExtractor を直接使用してください
+ */
+export declare function postIngestProcessing(repository: KnowledgeRepository, graphRepository: GraphRepository, onProgress?: (current: number, total: number) => void): Promise<PostIngestSummary>;
+//# sourceMappingURL=entity-extractor.d.ts.map

package/dist/lib/entity-extractor.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"entity-extractor.d.ts","sourceRoot":"","sources":["../../src/lib/entity-extractor.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,eAAe,EAAwB,MAAM,mBAAmB,CAAC;AAE/F,MAAM,WAAW,iBAAiB;IAChC,UAAU,EAAE,MAAM,CAAC;IACnB,cAAc,EAAE,MAAM,CAAC;IACvB,aAAa,EAAE,MAAM,CAAC;IACtB,cAAc,EAAE,MAAM,CAAC;IACvB,aAAa,EAAE,MAAM,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,UAAU,EAAE,mBAAmB,EAC/B,eAAe,EAAE,eAAe,EAChC,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,GACpD,OAAO,CAAC,iBAAiB,CAAC,CAe5B"}

package/dist/lib/entity-extractor.js

@@ -0,0 +1,22 @@
+import { KnowledgeRepository, GraphRepository, IncrementalExtractor } from "@knowledgine/core";
+/**
+ * 全ノートに対してパターン抽出、エンティティ抽出、関係推論をバッチ実行する。
+ * init コマンドから ingest パイプライン経由でノートが保存された後に呼ばれる。
+ *
+ * @deprecated 新規コードは IncrementalExtractor を直接使用してください
+ */
+export async function postIngestProcessing(repository, graphRepository, onProgress) {
+    const allNoteIds = repository.getAllNoteIds();
+    const totalNotes = allNoteIds.length;
+    const incrementalExtractor = new IncrementalExtractor(repository, graphRepository);
+    const summary = await incrementalExtractor.process(allNoteIds, onProgress);
+    return {
+        totalNotes,
+        processedNotes: summary.processedNotes,
+        totalEntities: summary.totalEntities,
+        totalRelations: summary.totalRelations,
+        totalPatterns: summary.totalPatterns,
+        errors: summary.errors,
+    };
+}
+//# sourceMappingURL=entity-extractor.js.map

package/dist/lib/entity-extractor.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"entity-extractor.js","sourceRoot":"","sources":["../../src/lib/entity-extractor.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAC;AAW/F;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,UAA+B,EAC/B,eAAgC,EAChC,UAAqD;IAErD,MAAM,UAAU,GAAG,UAAU,CAAC,aAAa,EAAE,CAAC;IAC9C,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;IAErC,MAAM,oBAAoB,GAAG,IAAI,oBAAoB,CAAC,UAAU,EAAE,eAAe,CAAC,CAAC;IACnF,MAAM,OAAO,GAAG,MAAM,oBAAoB,CAAC,OAAO,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;IAE3E,OAAO;QACL,UAAU;QACV,cAAc,EAAE,OAAO,CAAC,cAAc;QACtC,aAAa,EAAE,OAAO,CAAC,aAAa;QACpC,cAAc,EAAE,OAAO,CAAC,cAAc;QACtC,aAAa,EAAE,OAAO,CAAC,aAAa;QACpC,MAAM,EAAE,OAAO,CAAC,MAAM;KACvB,CAAC;AACJ,CAAC"}

package/dist/lib/formatter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"formatter.d.ts","sourceRoot":"","sources":["../../src/lib/formatter.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,qBAAqB,EACrB,iBAAiB,EACjB,WAAW,EACX,oBAAoB,EACrB,MAAM,mBAAmB,CAAC;AAG3B,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,OAAO,GAAG,OAAO,CAAC;AAEtD,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,qBAAqB,CAAC,SAAS,CAAC,EACzC,MAAM,EAAE,YAAY,GACnB,MAAM,CAeR;AAED,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,iBAAiB,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAsB1F;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAgC5E;AAED,wBAAgB,cAAc,CAAC,MAAM,EAAE,oBAAoB,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAazF"}
+{"version":3,"file":"formatter.d.ts","sourceRoot":"","sources":["../../src/lib/formatter.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,qBAAqB,EACrB,iBAAiB,EACjB,WAAW,EACX,oBAAoB,EACrB,MAAM,mBAAmB,CAAC;AAG3B,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,OAAO,GAAG,OAAO,CAAC;AAEtD,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,qBAAqB,CAAC,SAAS,CAAC,EACzC,MAAM,EAAE,YAAY,GACnB,MAAM,CAeR;AAED,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,iBAAiB,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAsB1F;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAyC5E;AAED,wBAAgB,cAAc,CAAC,MAAM,EAAE,oBAAoB,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAazF"}

package/dist/lib/formatter.js

@@ -43,13 +43,24 @@ export function formatStats(stats, format) {
     if (format === "json") {
         return JSON.stringify(stats, null, 2);
     }
+    const embeddingsGenerated = stats.embeddingStatus.notesWithoutEmbeddings !== null
+        ? stats.totalNotes - stats.embeddingStatus.notesWithoutEmbeddings
+        : null;
+    const embeddingCoverage = embeddingsGenerated !== null && stats.totalNotes > 0
+        ? Math.round((embeddingsGenerated / stats.totalNotes) * 100)
+        : null;
+    const embeddingDisplay = embeddingsGenerated !== null && embeddingCoverage !== null
+        ? `${embeddingsGenerated}/${stats.totalNotes} (${embeddingCoverage}%)`
+        : stats.embeddingStatus.available
+            ? "enabled"
+            : "disabled";
     if (format === "plain") {
         return [
             `Notes: ${stats.totalNotes}`,
             `Patterns: ${stats.totalPatterns}`,
             `Links: ${stats.totalLinks}`,
             `Pairs: ${stats.totalPairs}`,
-            `Embeddings: ${stats.embeddingStatus.available ? "enabled" : "disabled"}`,
+            `Embeddings: ${embeddingDisplay}`,
         ].join("\n");
     }
     // table
@@ -58,14 +69,8 @@ export function formatStats(stats, format) {
         ["Total Patterns", colors.info(String(stats.totalPatterns))],
         ["Total Links", colors.info(String(stats.totalLinks))],
         ["Total Pairs", colors.info(String(stats.totalPairs))],
-        ["Embeddings Available", colors.info(String(stats.embeddingStatus.available))],
+        ["Embeddings", colors.info(embeddingDisplay)],
     ];
-    if (stats.embeddingStatus.notesWithoutEmbeddings !== null) {
-        rows.push([
-            "Notes Without Embeddings",
-            colors.info(String(stats.embeddingStatus.notesWithoutEmbeddings)),
-        ]);
-    }
     if (stats.graphStats) {
         rows.push(["Graph Entities", colors.info(String(stats.graphStats.totalEntities))]);
         rows.push(["Graph Relations", colors.info(String(stats.graphStats.totalRelations))]);

package/dist/lib/formatter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"formatter.js","sourceRoot":"","sources":["../../src/lib/formatter.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAIhE,MAAM,UAAU,mBAAmB,CACjC,OAAyC,EACzC,MAAoB;IAEpB,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IAC1C,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,QAAQ,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC5F,CAAC;IACD,QAAQ;IACR,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IACpC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;QAC9B,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QACvC,CAAC,CAAC,KAAK;QACP,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC;KACvB,CAAC,CAAC;IACH,OAAO,WAAW,CAAC,EAAE,IAAI,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;AACjE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,MAAyB,EAAE,MAAoB;IAChF,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IACzC,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,MAAM,KAAK,GAAa,CAAC,YAAY,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;QACtD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,YAAY,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,QAAQ,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;QACpE,CAAC;QACD,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1B,CAAC;IACD,QAAQ;IACR,MAAM,MAAM,GAAG,4BAA4B,MAAM,CAAC,MAAM,GAAG,CAAC;IAC5D,IAAI,MAAM,CAAC,YAAY,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACrC,OAAO,GAAG,MAAM,8BAA8B,CAAC;IACjD,CAAC;IACD,MAAM,IAAI,GAAG,MAAM,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;QAC1C,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QACvC,CAAC,CAAC,KAAK;QACP,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC;KACvB,CAAC,CAAC;IACH,OAAO,GAAG,MAAM,KAAK,WAAW,CAAC,EAAE,IAAI,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC;AACjF,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAkB,EAAE,MAAoB;IAClE,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IACxC,CAAC;IACD,MAAM,mBAAmB,GACvB,KAAK,CAAC,eAAe,CAAC,sBAAsB,KAAK,IAAI;QACnD,CAAC,CAAC,KAAK,CAAC,UAAU,GAAG,KAAK,CAAC,eAAe,CAAC,sBAAsB;QACjE,CAAC,CAAC,IAAI,CAAC;IACX,MAAM,iBAAiB,GACrB,mBAAmB,KAAK,IAAI,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC;QAClD,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,mBAAmB,GAAG,KAAK,CAAC,UAAU,CAAC,GAAG,GAAG,CAAC;QAC5D,CAAC,CAAC,IAAI,CAAC;IACX,MAAM,gBAAgB,GACpB,mBAAmB,KAAK,IAAI,IAAI,iBAAiB,KAAK,IAAI;QACxD,CAAC,CAAC,GAAG,mBAAmB,IAAI,KAAK,CAAC,UAAU,KAAK,iBAAiB,IAAI;QACtE,CAAC,CAAC,KAAK,CAAC,eAAe,CAAC,SAAS;YAC/B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,UAAU,CAAC;IAEnB,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO;YACL,UAAU,KAAK,CAAC,UAAU,EAAE;YAC5B,aAAa,KAAK,CAAC,aAAa,EAAE;YAClC,UAAU,KAAK,CAAC,UAAU,EAAE;YAC5B,UAAU,KAAK,CAAC,UAAU,EAAE;YAC5B,eAAe,gBAAgB,EAAE;SAClC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACf,CAAC;IACD,QAAQ;IACR,MAAM,IAAI,GAAe;QACvB,CAAC,aAAa,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC;QACtD,CAAC,gBAAgB,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC;QAC5D,CAAC,aAAa,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC;QACtD,CAAC,aAAa,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC;QACtD,CAAC,YAAY,EAAE,MAAM,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;KAC9C,CAAC;IACF,IAAI,KAAK,CAAC,UAAU,EAAE,CAAC;QACrB,IAAI,CAAC,IAAI,CAAC,CAAC,gBAAgB,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC;QACnF,IAAI,CAAC,IAAI,CAAC,CAAC,iBAAiB,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC;IACvF,CAAC;IACD,OAAO,WAAW,CAAC,EAAE,IAAI,EAAE,CAAC,QAAQ,EAAE,OAAO,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;AAC1D,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAA4B,EAAE,MAAoB;IAC/E,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IACzC,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,MAAM,CAAC,QAAQ;aACnB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,UAAU,KAAK,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;aACrF,IAAI,CAAC,IAAI,CAAC,CAAC;IAChB,CAAC;IACD,QAAQ;IACR,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IAC7F,OAAO,WAAW,CAAC,EAAE,IAAI,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;AAC7D,CAAC"}

package/dist/templates/skills/knowledgine-explain/references.d.ts

@@ -0,0 +1,2 @@
+export declare const REFERENCES: Record<string, string>;
+//# sourceMappingURL=references.d.ts.map

package/dist/templates/skills/knowledgine-explain/references.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"references.d.ts","sourceRoot":"","sources":["../../../../src/templates/skills/knowledgine-explain/references.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAsL7C,CAAC"}

package/dist/templates/skills/knowledgine-explain/references.js

@@ -0,0 +1,183 @@
+export const REFERENCES = {
+    "entity-types.md": `# Entity Types
+
+The entity types recognized and extracted by knowledgine from knowledge base content.
+
+---
+
+## Core Entity Types
+
+| Type | Description | Examples |
+|------|-------------|---------|
+| \`technology\` | Libraries, frameworks, tools, languages | \`SQLite\`, \`TypeScript\`, \`Node.js\`, \`Zod\` |
+| \`concept\` | Abstract ideas, patterns, architectural concepts | \`caching\`, \`ESM\`, \`FTS5\`, \`semantic search\` |
+| \`project\` | Projects, repositories, products | \`knowledgine\`, \`claude-code\` |
+| \`person\` | Authors, contributors, contacts | Team members, external contributors |
+| \`component\` | Code components, classes, modules | \`KnowledgeRepository\`, \`IngestEngine\` |
+| \`command\` | CLI commands or API operations | \`knowledgine init\`, \`capture_knowledge\` |
+| \`file\` | Source files and paths | \`packages/core/src/config/config-loader.ts\` |
+| \`error\` | Named error types or error messages | \`SQLITE_CONSTRAINT\`, \`ENOENT\` |
+
+---
+
+## Searching for Entities
+
+### By exact name
+\`\`\`
+search_entities(query: "SQLite")
+search_entities(query: "KnowledgeRepository")
+\`\`\`
+
+### By type + name
+\`\`\`
+search_entities(query: "technology sqlite")
+search_entities(query: "concept caching")
+\`\`\`
+
+### By partial name
+\`\`\`
+search_entities(query: "Knowledge")  // matches KnowledgeRepository, knowledgine, etc.
+\`\`\`
+
+---
+
+## Entity Extraction Quality
+
+Entities are extracted automatically from note content using NLP. The quality depends
+on the clarity of the notes. If you notice missing or incorrect entities, use
+\`knowledgine-feedback\` to report them.
+
+**Common extraction issues**:
+- Abbreviations (TS → TypeScript may not be linked)
+- Generic words that happen to be class names (Table, Manager)
+- Multi-word entities where only part is captured
+
+---
+
+## Using Entities for Exploration
+
+Entities serve as navigation hubs in the knowledge graph. A technology entity like
+\`SQLite\` connects to every note that mentions SQLite, allowing you to traverse from
+the entity to all related bug fixes, design decisions, and patterns.
+
+**Exploration pattern**:
+\`\`\`
+1. search_entities(query: "SQLite") → get entity ID
+2. get_entity_graph(entityId: "<id>") → see all connections
+3. find_related(noteId: "<connected note id>") → traverse outward
+\`\`\`
+`,
+    "graph-navigation.md": `# Graph Navigation
+
+How to traverse the knowledge graph effectively using \`get_entity_graph\` and
+\`find_related\`.
+
+---
+
+## Knowledge Graph Structure
+
+The knowledge graph has two node types:
+
+- **Notes** — Individual knowledge entries (bug fixes, decisions, patterns, etc.)
+- **Entities** — Named things extracted from notes (technologies, concepts, people)
+
+**Edge types**:
+- Note → Entity: "this note mentions this entity"
+- Entity → Note: "this entity appears in these notes"
+- Note → Note: "these notes share entities" (implicit through entity connections)
+
+---
+
+## get_entity_graph
+
+Returns the entity and all notes it appears in, plus related entities.
+
+\`\`\`
+get_entity_graph(entityId: "123")
+// Returns: { entity, notes: [...], relatedEntities: [...] }
+
+get_entity_graph(entityName: "SQLite")
+// Look up entity by name then return graph
+\`\`\`
+
+**Use this when you want to**:
+- See every note about a specific technology or concept
+- Discover which other entities co-appear with this entity
+- Get an overview before doing deeper traversal
+
+---
+
+## find_related
+
+Returns notes related to a starting point (note or file path) via shared entities.
+
+\`\`\`
+find_related(noteId: "abc123", limit: 10, maxHops: 2)
+find_related(filePath: "src/commands/setup.ts", limit: 10)
+\`\`\`
+
+**Parameters**:
+- \`noteId\` or \`filePath\`: Starting point for traversal
+- \`limit\`: Maximum notes to return
+- \`maxHops\`: How many edge-traversal steps to allow (1–3)
+
+### maxHops Guide
+
+| maxHops | Meaning | When to use |
+|---------|---------|-------------|
+| 1 | Only notes that share a direct entity with the starting note | Focused lookup |
+| 2 | Notes 2 hops away (share an entity with a 1-hop note) | Default, good balance |
+| 3 | Notes 3 hops away | Open-ended exploration, large graph |
+
+**Higher maxHops returns more results but with lower average relevance.** Start at 1
+or 2 and increase only if the results are too sparse.
+
+---
+
+## Navigation Patterns
+
+### Pattern 1: Technology Deep Dive
+
+\`\`\`
+// Understand everything in the knowledge base about TypeScript
+1. search_entities(query: "TypeScript") → { id: "42", name: "TypeScript" }
+2. get_entity_graph(entityId: "42")
+   → 15 notes mention TypeScript
+   → related entities: ESM, tsconfig, type-safety
+3. find_related(noteId: "<top note id>", maxHops: 2)
+   → Surface adjacent notes
+\`\`\`
+
+### Pattern 2: Component History
+
+\`\`\`
+// Understand the history of the setup command
+1. search_entities(query: "setupCommand") → entity
+2. get_entity_graph(entityId: "<id>") → notes about setupCommand
+3. Filter for design-decision and refactoring notes
+4. Read chronologically to understand evolution
+\`\`\`
+
+### Pattern 3: Cross-Area Connections
+
+\`\`\`
+// Find connections between two components
+1. get_entity_graph(entityName: "IngestEngine") → set A of notes + entities
+2. get_entity_graph(entityName: "KnowledgeRepository") → set B
+3. Inspect overlap in relatedEntities to find bridges
+\`\`\`
+
+---
+
+## Interpreting Results
+
+When \`get_entity_graph\` returns many notes, prioritize by tag:
+
+| Priority | Tags |
+|----------|------|
+| High | \`design-decision\`, \`bug-fix\`, \`troubleshooting\` |
+| Medium | \`pattern\`, \`refactoring\`, \`external-knowledge\` |
+| Lower | Untagged notes |
+`,
+};
+//# sourceMappingURL=references.js.map

package/dist/templates/skills/knowledgine-explain/references.js.map

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package/dist/templates/skills/knowledgine-explain/skill-md.d.ts

@@ -0,0 +1,2 @@
+export declare const SKILL_MD = "---\nname: knowledgine-explain\ndescription: >\n  Explore entities, knowledge graph connections, and design history for unfamiliar\n  components. Invoke when exploring code you did not write, tracing the history of a\n  design decision, or understanding how a named entity (technology, library, project,\n  person) relates to other parts of the knowledge base.\n---\n# knowledgine-explain\n\n## Purpose\n\nTrace the knowledge graph to understand why things are the way they are. Explain uses\nentity search and graph traversal to surface the full context around a component or\nconcept \u2014 not just what exists, but how it connects to other parts of the system and\nwhat decisions shaped it.\n\n## When to Use\n\n- **Exploring unfamiliar code** \u2014 Who wrote what and why? What decisions shaped this?\n- **Understanding design rationale** \u2014 What alternatives were considered?\n- **Tracing knowledge provenance** \u2014 Where did this pattern or approach come from?\n- **Auditing a technology choice** \u2014 Why is this library used here?\n- **Understanding relationships** \u2014 How do components A and B relate?\n\n## When NOT to Use\n\n- When you just need to find a specific past solution (use knowledgine-recall instead)\n- When the entity does not exist in the knowledge base yet\n- For trivial well-known concepts with no project-specific context\n\n## How to Explain (MCP Tools)\n\n### Step 1: Search for entities\n\n```\nsearch_entities(\n  query: string,   // Entity name, technology, concept, or person\n  limit?: number   // Max results (default 10)\n)\n```\n\n### Step 2: Explore entity graph\n\n```\nget_entity_graph(\n  entityId?: string,    // ID from search_entities result\n  entityName?: string   // Or search by name directly\n)\n```\n\n### Step 3: Find related notes\n\n```\nfind_related(\n  noteId?: string,    // A relevant note ID found in earlier steps\n  filePath?: string,  // Or a relevant file path\n  limit?: number,\n  maxHops?: number    // 1\u20133, default 2\n)\n```\n\n## How to Explain (CLI Alternative)\n\n```bash\nknowledgine explain \"<entity name or concept>\"\n```\n\n## Step-by-Step Instructions\n\n1. **Identify the subject** \u2014 What entity, component, or concept do you want to understand?\n2. **Search for the entity** \u2014 Call `search_entities` with the subject name\n3. **Inspect the entity graph** \u2014 Call `get_entity_graph` with the entity ID\n4. **Traverse related notes** \u2014 Call `find_related` for notes that mention this entity\n5. **Synthesize findings** \u2014 Summarize what you learned about the entity's history and connections\n\n## Best Practices\n\n- Start with `search_entities` to discover the exact entity name as stored in the knowledge base\n- Use `get_entity_graph` to map the neighborhood before diving into individual notes\n- Increase `maxHops` gradually \u2014 start at 1, go to 2 or 3 if the immediate neighborhood is sparse\n- Look specifically for notes tagged `design-decision` \u2014 they explain the \"why\"\n\n## Reference Files\n\n- See `entity-types.md` for the entity taxonomy used in knowledgine\n- See `graph-navigation.md` for how to traverse the knowledge graph effectively\n";
+//# sourceMappingURL=skill-md.d.ts.map

package/dist/templates/skills/knowledgine-explain/skill-md.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"skill-md.d.ts","sourceRoot":"","sources":["../../../../src/templates/skills/knowledgine-explain/skill-md.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,QAAQ,wnGAuFpB,CAAC"}

package/dist/templates/skills/knowledgine-explain/skill-md.js

@@ -0,0 +1,89 @@
+export const SKILL_MD = `---
+name: knowledgine-explain
+description: >
+  Explore entities, knowledge graph connections, and design history for unfamiliar
+  components. Invoke when exploring code you did not write, tracing the history of a
+  design decision, or understanding how a named entity (technology, library, project,
+  person) relates to other parts of the knowledge base.
+---
+# knowledgine-explain
+
+## Purpose
+
+Trace the knowledge graph to understand why things are the way they are. Explain uses
+entity search and graph traversal to surface the full context around a component or
+concept — not just what exists, but how it connects to other parts of the system and
+what decisions shaped it.
+
+## When to Use
+
+- **Exploring unfamiliar code** — Who wrote what and why? What decisions shaped this?
+- **Understanding design rationale** — What alternatives were considered?
+- **Tracing knowledge provenance** — Where did this pattern or approach come from?
+- **Auditing a technology choice** — Why is this library used here?
+- **Understanding relationships** — How do components A and B relate?
+
+## When NOT to Use
+
+- When you just need to find a specific past solution (use knowledgine-recall instead)
+- When the entity does not exist in the knowledge base yet
+- For trivial well-known concepts with no project-specific context
+
+## How to Explain (MCP Tools)
+
+### Step 1: Search for entities
+
+\`\`\`
+search_entities(
+  query: string,   // Entity name, technology, concept, or person
+  limit?: number   // Max results (default 10)
+)
+\`\`\`
+
+### Step 2: Explore entity graph
+
+\`\`\`
+get_entity_graph(
+  entityId?: string,    // ID from search_entities result
+  entityName?: string   // Or search by name directly
+)
+\`\`\`
+
+### Step 3: Find related notes
+
+\`\`\`
+find_related(
+  noteId?: string,    // A relevant note ID found in earlier steps
+  filePath?: string,  // Or a relevant file path
+  limit?: number,
+  maxHops?: number    // 1–3, default 2
+)
+\`\`\`
+
+## How to Explain (CLI Alternative)
+
+\`\`\`bash
+knowledgine explain "<entity name or concept>"
+\`\`\`
+
+## Step-by-Step Instructions
+
+1. **Identify the subject** — What entity, component, or concept do you want to understand?
+2. **Search for the entity** — Call \`search_entities\` with the subject name
+3. **Inspect the entity graph** — Call \`get_entity_graph\` with the entity ID
+4. **Traverse related notes** — Call \`find_related\` for notes that mention this entity
+5. **Synthesize findings** — Summarize what you learned about the entity's history and connections
+
+## Best Practices
+
+- Start with \`search_entities\` to discover the exact entity name as stored in the knowledge base
+- Use \`get_entity_graph\` to map the neighborhood before diving into individual notes
+- Increase \`maxHops\` gradually — start at 1, go to 2 or 3 if the immediate neighborhood is sparse
+- Look specifically for notes tagged \`design-decision\` — they explain the "why"
+
+## Reference Files
+
+- See \`entity-types.md\` for the entity taxonomy used in knowledgine
+- See \`graph-navigation.md\` for how to traverse the knowledge graph effectively
+`;
+//# sourceMappingURL=skill-md.js.map

package/dist/templates/skills/knowledgine-explain/skill-md.js.map

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+{"version":3,"file":"skill-md.js","sourceRoot":"","sources":["../../../../src/templates/skills/knowledgine-explain/skill-md.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAuFvB,CAAC"}

package/dist/templates/skills/knowledgine-recall/references.d.ts

@@ -0,0 +1,2 @@
+export declare const REFERENCES: Record<string, string>;
+//# sourceMappingURL=references.d.ts.map

package/dist/templates/skills/knowledgine-recall/references.d.ts.map

@@ -0,0 +1 @@
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