@jcode.labs/mimir 0.4.5 → 0.4.7

package/README.md

@@ -17,7 +17,7 @@ same evidence through:
 - the `kb` CLI;
 - a TypeScript library API;
 - a local MCP stdio server for compatible AI agents;
-- portable agent skills copied by `kb setup`.
+- portable agent skills copied by `kb setup`, including audio and Markdown-report workflows.
 
 Mimir does not send documents to a hosted RAG service and does not generate final LLM answers in
 core. It returns cited retrieval context so the agent or model you trust can write from local
@@ -44,9 +44,9 @@ pnpm exec kb search "your question"
 pnpm exec kb ask "your question"
 ```
 
-By default, Mimir indexes documents from `private/`, stores generated state under `.kb/`, and keeps
-agent integration files under `.mimir/`. `kb setup` adds the matching Git ignore entries for local
-generated and private data.
+By default, Mimir indexes documents from `private/`, reports unsupported/skipped files during
+ingestion, stores generated state under `.kb/`, and keeps agent integration files under `.mimir/`.
+`kb setup` adds the matching Git ignore entries for local generated and private data.
 
 Run `pnpm exec kb doctor --fix` later to repair missing setup or rebuild stale indexes.
 
@@ -57,6 +57,12 @@ Run `pnpm exec kb doctor --fix` later to repair missing setup or rebuild stale i
 - MCP server: `pnpm exec kb serve-mcp`
 - Bundled skills: `pnpm exec kb setup` or `pnpm exec kb install-skill`
 
+## Claude Code And Codex
+
+After `pnpm exec kb setup`, use `.mimir/claude-mcp-server.json` with `claude mcp add-json`, or copy
+`.mimir/codex-mcp.toml` into a trusted Codex config layer. See the canonical GitHub README for the
+full agent demo.
+
 ## License
 
 MIT (c) Jean-Baptiste Thery.

package/dist/cli.js

@@ -93,7 +93,12 @@ program
     .option("--rebuild", "Accepted for compatibility; ingest always rebuilds the local index.")
     .action(async () => {
     const result = await ingest({ cwd: process.cwd(), rebuild: true });
-    console.log(pc.green(`Done. indexedFiles=${result.indexedFiles} chunks=${result.chunks} skippedFiles=${result.skippedFiles} redactions=${result.redactions} errors=${result.errors.length}`));
+    console.log(pc.green(`Done. discoveredFiles=${result.discoveredFiles} supportedFiles=${result.supportedFiles} indexedFiles=${result.indexedFiles} chunks=${result.chunks} skippedFiles=${result.skippedFiles} unsupportedFiles=${result.unsupportedFiles} oversizedFiles=${result.oversizedFiles} sensitiveFiles=${result.sensitiveFiles} redactions=${result.redactions} errors=${result.errors.length}`));
+    printUnsupportedSummary(result.unsupportedExtensions);
+    if (result.unsupportedFiles > 0 || result.oversizedFiles > 0 || result.sensitiveFiles > 0) {
+        const auditCommand = await kbCommand(process.cwd(), ["audit", "--unsupported"]);
+        console.log(pc.yellow(`Some files were not indexed. Run \`${auditCommand.display}\` for details.`));
+    }
     for (const error of result.errors) {
         console.error(pc.red(`  - ${error.path}: ${error.message}`));
     }
@@ -138,19 +143,36 @@ program
 program
     .command("audit")
     .description("Compare supported files on disk with the current vector index.")
-    .action(async () => {
+    .option("--unsupported", "List skipped file paths and reasons.")
+    .option("--json", "Print machine-readable JSON.")
+    .action(async (options) => {
     const report = await audit(process.cwd());
+    if (options.json) {
+        console.log(JSON.stringify(report, null, 2));
+        return;
+    }
     console.log(`supportedFiles=${report.supportedFiles.length}`);
+    console.log(`skippedFiles=${report.skippedFiles.length}`);
+    console.log(`unsupportedFiles=${report.skippedFiles.filter((file) => file.reason === "unsupported-extension").length}`);
     console.log(`indexedFiles=${report.indexedFiles.length}`);
     console.log(`totalChunks=${report.totalChunks}`);
     console.log(`missingFromIndex=${report.missingFromIndex.length}`);
     console.log(`staleInIndex=${report.staleInIndex.length}`);
+    printUnsupportedSummary(report.unsupportedExtensions);
     for (const file of report.missingFromIndex) {
         console.log(pc.yellow(`missing: ${file}`));
     }
     for (const file of report.staleInIndex) {
         console.log(pc.red(`stale: ${file}`));
     }
+    if (options.unsupported) {
+        for (const file of report.skippedFiles) {
+            console.log(pc.yellow(`skipped: ${file.relativePath} reason=${file.reason}`));
+        }
+    }
+    else if (report.skippedFiles.length > 0) {
+        console.log(pc.yellow("Run `kb audit --unsupported` to list skipped file paths."));
+    }
     if (report.missingFromIndex.length > 0 || report.staleInIndex.length > 0) {
         process.exitCode = 1;
     }
@@ -173,6 +195,9 @@ program
     console.log(`redactionEnabled=${config.redaction.enabled}`);
     console.log(`accessLog=${config.accessLog}`);
     console.log(`mcpMaxTopK=${config.mcpMaxTopK}`);
+    console.log(`maxFileBytes=${config.maxFileBytes}`);
+    console.log(`ingestConcurrency=${config.ingestConcurrency}`);
+    console.log(`embeddingBatchSize=${config.embeddingBatchSize}`);
     console.log(`includeExtensions=${config.includeExtensions.join(",")}`);
     console.log(`chunksIndexed=${rows}`);
 });
@@ -271,7 +296,7 @@ program
     .command("serve-mcp")
     .description("Start the MCP server over stdio for Claude, Codex, and other MCP-compatible agents.")
     .action(async () => {
-    await serveMcp(process.cwd());
+    await serveMcp();
 });
 program
     .command("skill-path")
@@ -292,10 +317,13 @@ program
     }
     console.log(`Skill path: ${result.skillPath}`);
     console.log(`Optional audio skill path: ${result.audioSkillPath}`);
+    console.log(`Optional Markdown report skill path: ${result.reportSkillPath}`);
     console.log(`MCP config example: ${result.mcpConfigPath}`);
+    console.log(`Claude Code MCP server JSON: ${result.claudeConfigPath}`);
+    console.log(`Codex MCP TOML snippet: ${result.codexConfigPath}`);
     console.log("");
     console.log("Next steps:");
-    console.log("  1. Add the MCP config from .mimir/mcp.json to your agent if it supports MCP.");
+    console.log("  1. Add the MCP config from .mimir/ to Claude Code, Codex, or another MCP client.");
     console.log("  2. Load .mimir/skills/mimir/ in agents that support skill folders.");
     console.log(`  3. Run \`${doctorCommand.display}\` before relying on retrieved context.`);
 });
@@ -374,6 +402,8 @@ function printDoctor(report) {
     console.log(`redactionEnabled=${report.redactionEnabled}`);
     console.log(`accessLog=${report.accessLog}`);
     console.log(`supportedFiles=${report.supportedFiles}`);
+    console.log(`skippedFiles=${report.skippedFiles}`);
+    console.log(`unsupportedFiles=${report.unsupportedFiles}`);
     console.log(`indexedFiles=${report.indexedFiles}`);
     console.log(`chunksIndexed=${report.chunksIndexed}`);
     console.log(`missingFromIndex=${report.missingFromIndex}`);
@@ -408,11 +438,18 @@ function printSetup(result, title) {
     console.log(pc.cyan("Agent integration:"));
     console.log(`  - skill: ${result.agentKit.skillPath}`);
     console.log(`  - audio skill: ${result.agentKit.audioSkillPath}`);
+    console.log(`  - report skill: ${result.agentKit.reportSkillPath}`);
     console.log(`  - MCP config: ${result.agentKit.mcpConfigPath}`);
+    console.log(`  - Claude Code MCP JSON: ${result.agentKit.claudeConfigPath}`);
+    console.log(`  - Codex MCP TOML: ${result.agentKit.codexConfigPath}`);
     console.log("");
     console.log(pc.cyan("Index:"));
     if (result.ingested) {
-        console.log(`  - ingested indexedFiles=${result.ingested.indexedFiles} chunks=${result.ingested.chunks} errors=${result.ingested.errors.length}`);
+        console.log(`  - ingested indexedFiles=${result.ingested.indexedFiles} chunks=${result.ingested.chunks} skippedFiles=${result.ingested.skippedFiles} errors=${result.ingested.errors.length}`);
+        printUnsupportedSummary(result.ingested.unsupportedExtensions);
+    }
+    else if (result.doctor.ready) {
+        console.log(`  - already ready chunks=${result.doctor.chunksIndexed}`);
     }
     else {
         console.log("  - skipped; add supported files or run doctor --fix when ready");
@@ -420,6 +457,14 @@ function printSetup(result, title) {
     console.log("");
     printDoctor(result.doctor);
 }
+function printUnsupportedSummary(extensions) {
+    if (extensions.length === 0) {
+        return;
+    }
+    console.log(pc.yellow(`unsupportedExtensions=${extensions
+        .map((entry) => `${entry.extension}:${entry.count}`)
+        .join(",")}`));
+}
 function printMaybeJson(value, json) {
     if (json) {
         console.log(JSON.stringify(value, null, 2));

package/dist/cli.js.map

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package/dist/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAwCxC,wBAAgB,eAAe,CAAC,KAAK,SAAgB,GAAG,MAAM,CAc7D;AAED,wBAAsB,UAAU,CAAC,KAAK,SAAgB,GAAG,OAAO,CAAC,MAAM,CAAC,CA+BvE"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AA2CxC,wBAAgB,eAAe,CAAC,KAAK,SAAgB,GAAG,MAAM,CAc7D;AAED,wBAAsB,UAAU,CAAC,KAAK,SAAgB,GAAG,OAAO,CAAC,MAAM,CAAC,CAkCvE"}

package/dist/config.js

@@ -33,6 +33,9 @@ const rawConfigSchema = z.object({
     topK: z.number().int().positive().default(DEFAULT_CONFIG.topK),
     chunkSize: z.number().int().positive().default(DEFAULT_CONFIG.chunkSize),
     chunkOverlap: z.number().int().nonnegative().default(DEFAULT_CONFIG.chunkOverlap),
+    maxFileBytes: z.number().int().positive().default(DEFAULT_CONFIG.maxFileBytes),
+    ingestConcurrency: z.number().int().positive().default(DEFAULT_CONFIG.ingestConcurrency),
+    embeddingBatchSize: z.number().int().positive().default(DEFAULT_CONFIG.embeddingBatchSize),
     includeExtensions: z.array(z.string().min(1)).default(DEFAULT_CONFIG.includeExtensions),
 });
 export function findProjectRoot(start = process.cwd()) {
@@ -74,6 +77,9 @@ export async function loadConfig(start = process.cwd()) {
         topK: withEnv.topK,
         chunkSize: withEnv.chunkSize,
         chunkOverlap: withEnv.chunkOverlap,
+        maxFileBytes: withEnv.maxFileBytes,
+        ingestConcurrency: withEnv.ingestConcurrency,
+        embeddingBatchSize: withEnv.embeddingBatchSize,
         includeExtensions: normalizeExtensions(withEnv.includeExtensions),
     };
 }
@@ -101,6 +107,9 @@ function applyEnv(config) {
         topK: readPositiveIntEnv("KB_TOP_K", config.topK),
         chunkSize: readPositiveIntEnv("KB_CHUNK_SIZE", config.chunkSize),
         chunkOverlap: readNonNegativeIntEnv("KB_CHUNK_OVERLAP", config.chunkOverlap),
+        maxFileBytes: readPositiveIntEnv("KB_MAX_FILE_BYTES", config.maxFileBytes),
+        ingestConcurrency: readPositiveIntEnv("KB_INGEST_CONCURRENCY", config.ingestConcurrency),
+        embeddingBatchSize: readPositiveIntEnv("KB_EMBEDDING_BATCH_SIZE", config.embeddingBatchSize),
         includeExtensions: readExtensionsEnv("KB_INCLUDE_EXTENSIONS", config.includeExtensions),
     };
 }

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/defaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"defaults.d.ts","sourceRoot":"","sources":["../src/defaults.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAExC,eAAO,MAAM,MAAM,QAAQ,CAAA;AAC3B,eAAO,MAAM,SAAS,WAAW,CAAA;AACjC,eAAO,MAAM,WAAW,YAAY,CAAA;AACpC,eAAO,MAAM,WAAW,oBAA0B,CAAA;AAClD,eAAO,MAAM,wBAAwB,kBAAwB,CAAA;AAE7D,eAAO,MAAM,kBAAkB,SAAe,CAAA;AAC9C,eAAO,MAAM,qBAAqB,YAAkB,CAAA;AACpD,eAAO,MAAM,uBAAuB,eAAsB,CAAA;AAE1D,eAAO,MAAM,cAAc,EAAE,IAAI,CAAC,MAAM,EAAE,aAAa,CAqBtD,CAAA"}
+{"version":3,"file":"defaults.d.ts","sourceRoot":"","sources":["../src/defaults.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAExC,eAAO,MAAM,MAAM,QAAQ,CAAA;AAC3B,eAAO,MAAM,SAAS,WAAW,CAAA;AACjC,eAAO,MAAM,WAAW,YAAY,CAAA;AACpC,eAAO,MAAM,WAAW,oBAA0B,CAAA;AAClD,eAAO,MAAM,wBAAwB,kBAAwB,CAAA;AAE7D,eAAO,MAAM,kBAAkB,SAAe,CAAA;AAC9C,eAAO,MAAM,qBAAqB,YAAkB,CAAA;AACpD,eAAO,MAAM,uBAAuB,eAAsB,CAAA;AAE1D,eAAO,MAAM,cAAc,EAAE,IAAI,CAAC,MAAM,EAAE,aAAa,CAwBtD,CAAA"}

package/dist/defaults.js

@@ -26,6 +26,9 @@ export const DEFAULT_CONFIG = {
     topK: 5,
     chunkSize: 1200,
     chunkOverlap: 150,
+    maxFileBytes: 50_000_000,
+    ingestConcurrency: 4,
+    embeddingBatchSize: 32,
     includeExtensions: [],
 };
 //# sourceMappingURL=defaults.js.map

package/dist/defaults.js.map

@@ -1 +1 @@
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+{"version":3,"file":"defaults.js","sourceRoot":"","sources":["../src/defaults.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,MAAM,MAAM,GAAG,KAAK,CAAA;AAC3B,MAAM,CAAC,MAAM,SAAS,GAAG,QAAQ,CAAA;AACjC,MAAM,CAAC,MAAM,WAAW,GAAG,SAAS,CAAA;AACpC,MAAM,CAAC,MAAM,WAAW,GAAG,GAAG,MAAM,cAAc,CAAA;AAClD,MAAM,CAAC,MAAM,wBAAwB,GAAG,GAAG,SAAS,SAAS,CAAA;AAE7D,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,MAAM,GAAG,CAAA;AAC9C,MAAM,CAAC,MAAM,qBAAqB,GAAG,GAAG,SAAS,GAAG,CAAA;AACpD,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,WAAW,KAAK,CAAA;AAE1D,MAAM,CAAC,MAAM,cAAc,GAAgC;IACzD,MAAM,EAAE,WAAW;IACnB,UAAU,EAAE,GAAG,MAAM,UAAU;IAC/B,WAAW,EAAE,GAAG,MAAM,cAAc;IACpC,aAAa,EAAE,GAAG,MAAM,aAAa;IACrC,kBAAkB,EAAE,GAAG,SAAS,SAAS;IACzC,SAAS,EAAE,QAAQ;IACnB,iBAAiB,EAAE,YAAY;IAC/B,cAAc,EAAE,qCAAqC;IACrD,6BAA6B,EAAE,KAAK;IACpC,SAAS,EAAE;QACT,OAAO,EAAE,IAAI;QACb,OAAO,EAAE,IAAI;QACb,QAAQ,EAAE,EAAE;KACb;IACD,SAAS,EAAE,IAAI;IACf,UAAU,EAAE,EAAE;IACd,IAAI,EAAE,CAAC;IACP,SAAS,EAAE,IAAI;IACf,YAAY,EAAE,GAAG;IACjB,YAAY,EAAE,UAAU;IACxB,iBAAiB,EAAE,CAAC;IACpB,kBAAkB,EAAE,EAAE;IACtB,iBAAiB,EAAE,EAAE;CACtB,CAAA"}

package/dist/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AAQA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAA;AAE9C,wBAAsB,MAAM,CAAC,GAAG,SAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,CAiDvE"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AAQA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAA;AAE9C,wBAAsB,MAAM,CAAC,GAAG,SAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,CAyDvE"}

package/dist/doctor.js

@@ -20,6 +20,8 @@ export async function doctor(cwd = process.cwd()) {
     const nextSteps = nextActions({
         initialized,
         supportedFiles: auditReport.supportedFiles.length,
+        skippedFiles: auditReport.skippedFiles.length,
+        unsupportedFiles: auditReport.skippedFiles.filter((file) => file.reason === "unsupported-extension").length,
         chunksIndexed,
         missingFromIndex: auditReport.missingFromIndex.length,
         staleInIndex: auditReport.staleInIndex.length,
@@ -40,6 +42,8 @@ export async function doctor(cwd = process.cwd()) {
         redactionEnabled: config.redaction.enabled,
         accessLog: config.accessLog,
         supportedFiles: auditReport.supportedFiles.length,
+        skippedFiles: auditReport.skippedFiles.length,
+        unsupportedFiles: auditReport.skippedFiles.filter((file) => file.reason === "unsupported-extension").length,
         indexedFiles: auditReport.indexedFiles.length,
         chunksIndexed,
         missingFromIndex: auditReport.missingFromIndex.length,
@@ -60,7 +64,12 @@ function nextActions(input) {
         return steps;
     }
     if (input.supportedFiles === 0) {
-        steps.push("Add supported files under private/ or list extra source paths in .kb/sources.txt.");
+        if (input.skippedFiles > 0) {
+            steps.push("Mimir found files, but none are currently indexable. Run `kb audit --unsupported` to inspect skipped files.");
+        }
+        else {
+            steps.push("Add supported files under private/ or list extra source paths in .kb/sources.txt.");
+        }
         return steps;
     }
     if (input.chunksIndexed === 0 || input.missingFromIndex > 0 || input.staleInIndex > 0) {
@@ -71,6 +80,9 @@ function nextActions(input) {
         steps.push(`Run \`${input.run(["security-audit", "--strict"])}\` and fix the reported warnings.`);
     }
     if (steps.length === 0) {
+        if (input.unsupportedFiles > 0) {
+            steps.push("Run `kb audit --unsupported` to inspect files skipped because their type is not supported.");
+        }
         steps.push(`Run \`${input.run(["search", '"your question"'])}\` to retrieve source passages.`);
         steps.push(`Run \`${input.run(["ask", '"your question"'])}\` to produce cited retrieval context.`);
         if (input.agentKitInstalled) {
@@ -85,6 +97,9 @@ function nextActions(input) {
 function isAgentKitInstalled(projectRoot) {
     return (existsSync(path.join(projectRoot, MIMIR_DIR, "skills", "mimir", "SKILL.md")) &&
         existsSync(path.join(projectRoot, MIMIR_DIR, "skills", "mimir-audio-summary", "SKILL.md")) &&
-        existsSync(path.join(projectRoot, MIMIR_DIR, "mcp.json")));
+        existsSync(path.join(projectRoot, MIMIR_DIR, "skills", "mimir-markdown-report", "SKILL.md")) &&
+        existsSync(path.join(projectRoot, MIMIR_DIR, "mcp.json")) &&
+        existsSync(path.join(projectRoot, MIMIR_DIR, "claude-mcp-server.json")) &&
+        existsSync(path.join(projectRoot, MIMIR_DIR, "codex-mcp.toml")));
 }
 //# sourceMappingURL=doctor.js.map

package/dist/doctor.js.map

@@ -1 +1 @@
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package/dist/files.d.ts

@@ -1,5 +1,10 @@
-import type { Config, SourceFile } from "./types.js";
+import type { Config, SkippedSourceFile, SourceFile, SourceInventory } from "./types.js";
 export declare const DEFAULT_SUPPORTED_EXTENSIONS: Set<string>;
 export declare function listSourceFiles(config: Config): Promise<SourceFile[]>;
+export declare function inventorySourceFiles(config: Config): Promise<SourceInventory>;
 export declare function supportedExtensions(config: Config): Set<string>;
+export declare function summarizeUnsupportedExtensions(skippedFiles: SkippedSourceFile[]): Array<{
+    extension: string;
+    count: number;
+}>;
 //# sourceMappingURL=files.d.ts.map

package/dist/files.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"files.d.ts","sourceRoot":"","sources":["../src/files.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,MAAM,EAAE,iBAAiB,EAAE,UAAU,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAyBxF,eAAO,MAAM,4BAA4B,aAyEvC,CAAA;AAEF,wBAAsB,eAAe,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,UAAU,EAAE,CAAC,CAE3E;AAED,wBAAsB,oBAAoB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC,CAqFnF;AAED,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAE/D;AAED,wBAAgB,8BAA8B,CAC5C,YAAY,EAAE,iBAAiB,EAAE,GAChC,KAAK,CAAC;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAW7C"}