@knowledgine/cli 0.4.0 → 0.5.0

package/dist/commands/serve.js

@@ -2,7 +2,7 @@ import { Command } from "commander";
 import { existsSync } from "fs";
 import { resolve } from "path";
 import { serve } from "@hono/node-server";
-import { loadConfig, resolveDefaultPath, createDatabase, Migrator, ALL_MIGRATIONS, KnowledgeRepository, GraphRepository, KnowledgeService, VERSION, } from "@knowledgine/core";
+import { loadConfig, resolveDefaultPath, createDatabase, loadSqliteVecExtension, Migrator, ALL_MIGRATIONS, KnowledgeRepository, GraphRepository, KnowledgeService, OnnxEmbeddingProvider, ModelManager, DEFAULT_MODEL_NAME, VERSION, checkSemanticReadiness, } from "@knowledgine/core";
 import { createRestApp } from "@knowledgine/mcp-server";
 export function registerServeCommand(program) {
     program
@@ -27,11 +27,31 @@ async function serveAction(options) {
         new Migrator(db, ALL_MIGRATIONS).migrate();
         const repository = new KnowledgeRepository(db);
         const graphRepository = new GraphRepository(db);
-        const service = new KnowledgeService({ repository, rootPath, graphRepository });
+        // Auto-detect model for backward compatibility (without mutating config)
+        const modelManager = new ModelManager();
+        const autoDetected = !config.embedding?.enabled && modelManager.isModelAvailable(config.embedding?.modelName);
+        const effectiveConfig = autoDetected
+            ? { ...config, embedding: { ...config.embedding, enabled: true } }
+            : config;
+        // Initialize embedding provider based on actual semantic readiness
+        const semanticReadiness = checkSemanticReadiness(effectiveConfig, modelManager, repository);
+        let embeddingProvider;
+        if (semanticReadiness.ready) {
+            // Load sqlite-vec when semantic search is effectively enabled (config or auto-detected)
+            await loadSqliteVecExtension(db);
+            embeddingProvider = new OnnxEmbeddingProvider(DEFAULT_MODEL_NAME, modelManager);
+        }
+        const service = new KnowledgeService({
+            repository,
+            rootPath,
+            graphRepository,
+            embeddingProvider,
+        });
         const app = createRestApp(service, VERSION);
         const port = parseInt(options.port ?? "3456", 10);
         const hostname = options.host ?? "127.0.0.1";
         const stats = service.getStats();
+        const searchMode = embeddingProvider ? "semantic + FTS5" : "FTS5 only";
         const server = serve({
             fetch: app.fetch,
             port,
@@ -40,10 +60,14 @@ async function serveAction(options) {
             console.error(`knowledgine REST API server running`);
             console.error(`  URL:    http://${hostname}:${port}`);
             console.error(`  Notes:  ${stats.totalNotes} indexed`);
+            console.error(`  Search: ${searchMode}`);
         });
         // Graceful shutdown
-        const shutdown = () => {
+        const shutdown = async () => {
             console.error("\nShutting down...");
+            if (embeddingProvider) {
+                await embeddingProvider.close();
+            }
             server.close();
             db.close();
             process.exit(0);

package/dist/commands/serve.js.map

@@ -1 +1 @@
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+{"version":3,"file":"serve.js","sourceRoot":"","sources":["../../src/commands/serve.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,IAAI,CAAC;AAChC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC;AAC/B,OAAO,EAAE,KAAK,EAAE,MAAM,mBAAmB,CAAC;AAC1C,OAAO,EACL,UAAU,EACV,kBAAkB,EAClB,cAAc,EACd,sBAAsB,EACtB,QAAQ,EACR,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,gBAAgB,EAChB,qBAAqB,EACrB,YAAY,EACZ,kBAAkB,EAClB,OAAO,EACP,sBAAsB,GACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,aAAa,EAAE,MAAM,yBAAyB,CAAC;AAQxD,MAAM,UAAU,oBAAoB,CAAC,OAAgB;IACnD,OAAO;SACJ,OAAO,CAAC,OAAO,CAAC;SAChB,WAAW,CAAC,iDAAiD,CAAC;SAC9D,MAAM,CAAC,YAAY,EAAE,aAAa,EAAE,MAAM,CAAC;SAC3C,MAAM,CAAC,eAAe,EAAE,cAAc,EAAE,WAAW,CAAC;SACpD,MAAM,CAAC,cAAc,EAAE,mBAAmB,CAAC;SAC3C,MAAM,CAAC,WAAW,CAAC,CAAC;AACzB,CAAC;AAED,KAAK,UAAU,WAAW,CAAC,OAA4B;IACrD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAClD,MAAM,cAAc,GAAG,OAAO,CAAC,QAAQ,EAAE,cAAc,CAAC,CAAC;IAEzD,IAAI,CAAC,UAAU,CAAC,cAAc,CAAC,EAAE,CAAC;QAChC,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;QAC7E,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC;IACpC,MAAM,EAAE,GAAG,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAEzC,IAAI,CAAC;QACH,IAAI,QAAQ,CAAC,EAAE,EAAE,cAAc,CAAC,CAAC,OAAO,EAAE,CAAC;QAC3C,MAAM,UAAU,GAAG,IAAI,mBAAmB,CAAC,EAAE,CAAC,CAAC;QAC/C,MAAM,eAAe,GAAG,IAAI,eAAe,CAAC,EAAE,CAAC,CAAC;QAEhD,yEAAyE;QACzE,MAAM,YAAY,GAAG,IAAI,YAAY,EAAE,CAAC;QACxC,MAAM,YAAY,GAChB,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,IAAI,YAAY,CAAC,gBAAgB,CAAC,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;QAC3F,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,EAAE,GAAG,MAAM,EAAE,SAAS,EAAE,EAAE,GAAG,MAAM,CAAC,SAAS,EAAE,OAAO,EAAE,IAAI,EAAE,EAAE;YAClE,CAAC,CAAC,MAAM,CAAC;QAEX,mEAAmE;QACnE,MAAM,iBAAiB,GAAG,sBAAsB,CAAC,eAAe,EAAE,YAAY,EAAE,UAAU,CAAC,CAAC;QAC5F,IAAI,iBAAoD,CAAC;QACzD,IAAI,iBAAiB,CAAC,KAAK,EAAE,CAAC;YAC5B,wFAAwF;YACxF,MAAM,sBAAsB,CAAC,EAAE,CAAC,CAAC;YACjC,iBAAiB,GAAG,IAAI,qBAAqB,CAAC,kBAAkB,EAAE,YAAY,CAAC,CAAC;QAClF,CAAC;QAED,MAAM,OAAO,GAAG,IAAI,gBAAgB,CAAC;YACnC,UAAU;YACV,QAAQ;YACR,eAAe;YACf,iBAAiB;SAClB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,CAAC,IAAI,IAAI,MAAM,EAAE,EAAE,CAAC,CAAC;QAClD,MAAM,QAAQ,GAAG,OAAO,CAAC,IAAI,IAAI,WAAW,CAAC;QAE7C,MAAM,KAAK,GAAG,OAAO,CAAC,QAAQ,EAAE,CAAC;QACjC,MAAM,UAAU,GAAG,iBAAiB,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,WAAW,CAAC;QAEvE,MAAM,MAAM,GAAG,KAAK,CAClB;YACE,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,IAAI;YACJ,QAAQ;SACT,EACD,GAAG,EAAE;YACH,OAAO,CAAC,KAAK,CAAC,qCAAqC,CAAC,CAAC;YACrD,OAAO,CAAC,KAAK,CAAC,oBAAoB,QAAQ,IAAI,IAAI,EAAE,CAAC,CAAC;YACtD,OAAO,CAAC,KAAK,CAAC,aAAa,KAAK,CAAC,UAAU,UAAU,CAAC,CAAC;YACvD,OAAO,CAAC,KAAK,CAAC,aAAa,UAAU,EAAE,CAAC,CAAC;QAC3C,CAAC,CACF,CAAC;QAEF,oBAAoB;QACpB,MAAM,QAAQ,GAAG,KAAK,IAAI,EAAE;YAC1B,OAAO,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC;YACpC,IAAI,iBAAiB,EAAE,CAAC;gBACtB,MAAM,iBAAiB,CAAC,KAAK,EAAE,CAAC;YAClC,CAAC;YACD,MAAM,CAAC,KAAK,EAAE,CAAC;YACf,EAAE,CAAC,KAAK,EAAE,CAAC;YACX,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC,CAAC;QACF,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;QAC/B,OAAO,CAAC,EAAE,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IAClC,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,EAAE,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,UAAU,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAClF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;IACvB,CAAC;AACH,CAAC"}

package/dist/commands/setup-rules.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"setup-rules.d.ts","sourceRoot":"","sources":["../../src/commands/setup-rules.ts"],"names":[],"mappings":"AAqBA,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IACtC,QAAQ,EAAE,gBAAgB,GAAG,aAAa,CAAC;IAC3C,WAAW,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IACtC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,eAAe;IAC9B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,IAAI,GAAG,SAAS,GAAG,MAAM,CAAC;IAClC,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,eAAO,MAAM,YAAY,EAAE,UAAU,EA4HpC,CAAC;AAEF,wBAAgB,aAAa,CAC3B,MAAM,EAAE,UAAU,EAClB,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAC7C,eAAe,CAgEjB;AAED,wBAAsB,qBAAqB,CACzC,WAAW,EAAE,MAAM,EACnB,qBAAqB,CAAC,EAAE,MAAM,EAAE,GAC/B,OAAO,CAAC,eAAe,EAAE,CAAC,CAwF5B;AAED,wBAAgB,wBAAwB,CACtC,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAC3B,IAAI,CAkDN"}
+{"version":3,"file":"setup-rules.d.ts","sourceRoot":"","sources":["../../src/commands/setup-rules.ts"],"names":[],"mappings":"AAyBA,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IACtC,QAAQ,EAAE,gBAAgB,GAAG,aAAa,CAAC;IAC3C,WAAW,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IACtC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,eAAe;IAC9B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,IAAI,GAAG,SAAS,GAAG,MAAM,CAAC;IAClC,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,eAAO,MAAM,YAAY,EAAE,UAAU,EA4HpC,CAAC;AAEF,wBAAgB,aAAa,CAC3B,MAAM,EAAE,UAAU,EAClB,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAC7C,eAAe,CAiEjB;AAED,wBAAsB,qBAAqB,CACzC,WAAW,EAAE,MAAM,EACnB,qBAAqB,CAAC,EAAE,MAAM,EAAE,GAC/B,OAAO,CAAC,eAAe,EAAE,CAAC,CAwF5B;AAED,wBAAgB,wBAAwB,CACtC,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAC3B,IAAI,CAkDN"}

package/dist/commands/setup-rules.js

@@ -1,7 +1,7 @@
 import { join } from "path";
-import { existsSync, readFileSync, writeFileSync, mkdirSync, copyFileSync } from "fs";
 import * as p from "@clack/prompts";
 import { colors, symbols } from "../lib/ui/index.js";
+import { readTextFileIfExists, writeTextFileAtomically, writeTextFileExclusively, } from "../lib/file-utils.js";
 import { getClaudeCodeRuleTemplate, getCursorRuleTemplate, getWindsurfRuleTemplate, getClineRuleTemplate, getCodexRuleTemplate, getGithubCopilotRuleTemplate, getGeminiRuleTemplate, getContinueRuleTemplate, getZedRuleTemplate, getOpencodeRuleTemplate, getAntigravityRuleTemplate, } from "../templates/rules/index.js";
 const MARKER_START = "<!-- knowledgine:rules:start -->";
 const MARKER_END = "<!-- knowledgine:rules:end -->";
@@ -135,8 +135,8 @@ export function writeRuleFile(target, projectRoot, options) {
     const templateContent = target.getTemplate(projectRoot);
     if (target.strategy === "append-section") {
         let finalContent;
-        if (existsSync(filePath)) {
-            const existing = readFileSync(filePath, "utf-8");
+        const existing = readTextFileIfExists(filePath);
+        if (existing !== null) {
             const startIdx = existing.indexOf(MARKER_START);
             const endIdx = existing.indexOf(MARKER_END);
             if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
@@ -152,40 +152,41 @@ export function writeRuleFile(target, projectRoot, options) {
                 finalContent = trimmed ? trimmed + "\n\n" + templateContent + "\n" : templateContent + "\n";
             }
             if (!options.dryRun) {
-                copyFileSync(filePath, filePath + ".bak");
-                writeFileSync(filePath, finalContent, "utf-8");
+                writeTextFileAtomically(filePath, finalContent);
             }
         }
         else {
             finalContent = templateContent + "\n";
             if (!options.dryRun) {
-                const dir = join(filePath, "..");
-                if (!existsSync(dir)) {
-                    mkdirSync(dir, { recursive: true });
-                }
-                writeFileSync(filePath, finalContent, "utf-8");
+                writeTextFileAtomically(filePath, finalContent);
             }
         }
         return { target: target.label, status: "ok", filePath };
     }
     // create-file strategy
-    if (existsSync(filePath) && !options.force) {
-        return {
-            target: target.label,
-            status: "skipped",
-            filePath,
-            note: "File already exists. Use --force to overwrite.",
-        };
+    if (options.dryRun) {
+        if (!options.force && readTextFileIfExists(filePath) !== null) {
+            return {
+                target: target.label,
+                status: "skipped",
+                filePath,
+                note: "File already exists. Use --force to overwrite.",
+            };
+        }
+        return { target: target.label, status: "ok", filePath };
     }
     if (!options.dryRun) {
-        const dir = join(filePath, "..");
-        if (!existsSync(dir)) {
-            mkdirSync(dir, { recursive: true });
+        if (options.force) {
+            writeTextFileAtomically(filePath, templateContent);
         }
-        if (existsSync(filePath)) {
-            copyFileSync(filePath, filePath + ".bak");
+        else if (!writeTextFileExclusively(filePath, templateContent)) {
+            return {
+                target: target.label,
+                status: "skipped",
+                filePath,
+                note: "File already exists. Use --force to overwrite.",
+            };
         }
-        writeFileSync(filePath, templateContent, "utf-8");
     }
     return { target: target.label, status: "ok", filePath };
 }

package/dist/commands/setup-rules.js.map

@@ -1 +1 @@
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package/dist/commands/setup.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"setup.d.ts","sourceRoot":"","sources":["../../src/commands/setup.ts"],"names":[],"mappings":"AAUA,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAWD,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAcV,CAAC;AAOX,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CA6FpD;AAED,wBAAgB,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAGrD;AAqHD,eAAO,MAAM,sBAAsB,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,WAAW,EAAE,MAAM,KAAK,MAAM,CAMlF,CAAC;AAqJF,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC,cAAc,CAAC;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC,cAAc,CAAC;IAC/B,KAAK,EAAE,OAAO,CAAC;CAChB;AAED,wBAAsB,YAAY,CAChC,OAAO,EAAE,YAAY,EACrB,WAAW,CAAC,EAAE,OAAO,GAAG,OAAO,GAC9B,OAAO,CAAC,IAAI,CAAC,CAoIf"}
+{"version":3,"file":"setup.d.ts","sourceRoot":"","sources":["../../src/commands/setup.ts"],"names":[],"mappings":"AAWA,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAWD,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAcV,CAAC;AAOX,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CA6FpD;AAED,wBAAgB,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAGrD;AAgHD,eAAO,MAAM,sBAAsB,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,WAAW,EAAE,MAAM,KAAK,MAAM,CAMlF,CAAC;AAqJF,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC,cAAc,CAAC;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC,cAAc,CAAC;IAC/B,KAAK,EAAE,OAAO,CAAC;CAChB;AAED,wBAAsB,YAAY,CAChC,OAAO,EAAE,YAAY,EACrB,WAAW,CAAC,EAAE,OAAO,GAAG,OAAO,GAC9B,OAAO,CAAC,IAAI,CAAC,CAoIf"}

package/dist/commands/setup.js

@@ -1,5 +1,5 @@
 import { resolve, join } from "path";
-import { existsSync, readFileSync, writeFileSync, mkdirSync, copyFileSync } from "fs";
+import { existsSync } from "fs";
 import { homedir } from "os";
 import { resolveDefaultPath } from "@knowledgine/core";
 import { createBox, colors, symbols } from "../lib/ui/index.js";
@@ -7,6 +7,7 @@ import * as p from "@clack/prompts";
 import * as TOML from "smol-toml";
 import { interactiveRulesSetup, nonInteractiveRulesSetup } from "./setup-rules.js";
 import { interactiveSkillsSetup, nonInteractiveSkillsSetup } from "./setup-skills.js";
+import { readTextFileIfExists, writeTextFileAtomically } from "../lib/file-utils.js";
 export const TARGETS = [
     { value: "claude-desktop", label: "Claude Desktop", description: "Anthropic's desktop app" },
     { value: "cursor", label: "Cursor", description: "AI-first code editor" },
@@ -102,21 +103,22 @@ function getMcpKey(target) {
     return "mcpServers";
 }
 function readExistingConfig(configPath, target) {
-    if (!existsSync(configPath)) {
+    const raw = readTextFileIfExists(configPath);
+    if (raw === null) {
         return {};
     }
-    const raw = readFileSync(configPath, "utf-8").trim();
-    if (!raw) {
+    const trimmed = raw.trim();
+    if (!trimmed) {
         return {};
     }
     try {
         if (isTomlConfig(configPath)) {
-            const parsed = TOML.parse(raw);
+            const parsed = TOML.parse(trimmed);
             return {
                 mcpServers: (parsed["mcp_servers"] ?? {}),
             };
         }
-        const parsed = JSON.parse(raw);
+        const parsed = JSON.parse(trimmed);
         const mcpKey = getMcpKey(target ?? "");
         // For tools that embed MCP in a larger settings file (Zed, VS Code)
         if (parsed[mcpKey]) {
@@ -141,19 +143,13 @@ function mergeConfig(existing, rootPath) {
     };
 }
 function writeConfig(configPath, config, target) {
-    const configDir = resolve(configPath, "..");
-    if (!existsSync(configDir)) {
-        mkdirSync(configDir, { recursive: true });
-    }
-    if (existsSync(configPath)) {
-        copyFileSync(configPath, configPath + ".bak");
-    }
     if (isTomlConfig(configPath)) {
         // TOML: read existing, merge mcp_servers, write back
         let existing = {};
-        if (existsSync(configPath)) {
+        const raw = readTextFileIfExists(configPath);
+        if (raw !== null) {
             try {
-                existing = TOML.parse(readFileSync(configPath, "utf-8"));
+                existing = TOML.parse(raw);
             }
             catch {
                 /* start fresh */
@@ -163,7 +159,7 @@ function writeConfig(configPath, config, target) {
             ...(existing["mcp_servers"] ?? {}),
             knowledgine: config.mcpServers?.["knowledgine"] ?? buildMcpConfig(""),
         };
-        writeFileSync(configPath, TOML.stringify(existing) + "\n", "utf-8");
+        writeTextFileAtomically(configPath, TOML.stringify(existing) + "\n");
     }
     else {
         const mcpKey = getMcpKey(target ?? "");
@@ -171,9 +167,10 @@ function writeConfig(configPath, config, target) {
         if (isEmbeddedSettings) {
             // Zed/VS Code: merge into existing settings.json
             let existing = {};
-            if (existsSync(configPath)) {
+            const raw = readTextFileIfExists(configPath);
+            if (raw !== null) {
                 try {
-                    existing = JSON.parse(readFileSync(configPath, "utf-8"));
+                    existing = JSON.parse(raw);
                 }
                 catch {
                     /* start fresh */
@@ -183,10 +180,10 @@ function writeConfig(configPath, config, target) {
                 ...(existing[mcpKey] ?? {}),
                 knowledgine: config.mcpServers?.["knowledgine"] ?? buildMcpConfig(""),
             };
-            writeFileSync(configPath, JSON.stringify(existing, null, 2) + "\n", "utf-8");
+            writeTextFileAtomically(configPath, JSON.stringify(existing, null, 2) + "\n");
         }
         else {
-            writeFileSync(configPath, JSON.stringify(config, null, 2) + "\n", "utf-8");
+            writeTextFileAtomically(configPath, JSON.stringify(config, null, 2) + "\n");
         }
     }
 }

package/dist/commands/setup.js.map

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package/dist/commands/start.d.ts

@@ -1,6 +1,7 @@
 export interface StartOptions {
     path?: string;
     ingest?: boolean;
+    watch?: boolean;
 }
 export declare function startCommand(options: StartOptions): Promise<void>;
 //# sourceMappingURL=start.d.ts.map

package/dist/commands/start.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"start.d.ts","sourceRoot":"","sources":["../../src/commands/start.ts"],"names":[],"mappings":"AAuBA,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAqOvE"}
+{"version":3,"file":"start.d.ts","sourceRoot":"","sources":["../../src/commands/start.ts"],"names":[],"mappings":"AAwBA,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAgRvE"}