@jcode.labs/ragmir 2.17.2 → 2.18.0

package/dist/context-resources.js

@@ -1,9 +1,10 @@
 import { loadConfig } from "./config.js";
-import { doctor } from "./doctor.js";
-import { audit } from "./ingest.js";
+import { doctorWithConfig } from "./doctor.js";
 import { knowledgeBaseIdentity } from "./knowledge-bases.js";
 import { operationSignal, throwIfAborted } from "./operation.js";
+import { readIndexManifestFilePage, readIndexManifestHeader } from "./store.js";
 const SOURCE_CATALOG_LIMIT = 50;
+const MAX_SOURCE_CATALOG_LIMIT = 100;
 const RAGMIR_MCP_TOOLS = [
     "ragmir_status",
     "ragmir_route_prompt",
@@ -21,8 +22,12 @@ export async function getKnowledgeBaseContext(cwd = process.cwd(), options = {})
     const signal = operationSignal(options);
     throwIfAborted(signal);
     const config = await loadConfig(cwd);
+    return getKnowledgeBaseContextWithConfig(config, options);
+}
+export async function getKnowledgeBaseContextWithConfig(config, options = {}) {
+    const signal = operationSignal(options);
     throwIfAborted(signal);
-    const report = await doctor(config.projectRoot, signal ? { signal } : {});
+    const report = await doctorWithConfig(config, signal ? { signal } : {});
     throwIfAborted(signal);
     const identity = knowledgeBaseIdentity(config.projectRoot);
     return {
@@ -31,6 +36,7 @@ export async function getKnowledgeBaseContext(cwd = process.cwd(), options = {})
         privacyProfile: config.privacyProfile,
         retrievalProfile: config.retrievalProfile,
         embeddingProvider: config.embeddingProvider,
+        corpusFingerprint: report.corpusFingerprint,
         ready: report.ready,
         coverage: {
             supportedFiles: report.supportedFiles,
@@ -55,42 +61,67 @@ export async function getKnowledgeBaseSourceCatalog(cwd = process.cwd(), options
     const signal = operationSignal(options);
     throwIfAborted(signal);
     const config = await loadConfig(cwd);
+    return getKnowledgeBaseSourceCatalogWithConfig(config, options);
+}
+export async function getKnowledgeBaseSourceCatalogWithConfig(config, options = {}) {
+    const signal = operationSignal(options);
     throwIfAborted(signal);
-    const report = await audit(config.projectRoot, signal ? { signal } : {});
+    const offset = sourceCatalogOffset(options.offset);
+    const limit = sourceCatalogLimit(options.limit);
+    const [manifest, filePage] = await Promise.all([
+        readIndexManifestHeader(config),
+        readIndexManifestFilePage(config, offset, limit),
+    ]);
     throwIfAborted(signal);
     const identity = knowledgeBaseIdentity(config.projectRoot);
-    const indexedFiles = report.indexedFiles.slice(0, SOURCE_CATALOG_LIMIT);
-    const missingFromIndex = report.missingFromIndex.slice(0, SOURCE_CATALOG_LIMIT);
-    const staleInIndex = report.staleInIndex.slice(0, SOURCE_CATALOG_LIMIT);
-    const emptyTextFiles = report.emptyTextFiles.slice(0, SOURCE_CATALOG_LIMIT);
+    const health = manifest?.health;
+    const indexedFiles = (filePage?.files ?? []).map((file) => ({
+        source: file.relativePath,
+        chunks: file.chunkCount,
+    }));
+    const missingFromIndex = health?.previews.missingFromIndex.slice(0, limit) ?? [];
+    const staleInIndex = health?.previews.staleInIndex.slice(0, limit) ?? [];
+    const emptyTextFiles = health?.previews.emptyTextFiles.slice(0, limit) ?? [];
     return {
         knowledgeBaseId: identity?.id ?? null,
         totals: {
-            indexedFiles: report.indexedFiles.length,
-            chunks: report.totalChunks,
-            missingFromIndex: report.missingFromIndex.length,
-            staleInIndex: report.staleInIndex.length,
-            emptyTextFiles: report.emptyTextFiles.length,
-            skippedFiles: report.skippedFiles.length,
+            indexedFiles: manifest?.fileCount ?? 0,
+            chunks: manifest?.chunkCount ?? 0,
+            missingFromIndex: health?.missingFromIndex ?? 0,
+            staleInIndex: health?.staleInIndex ?? 0,
+            emptyTextFiles: health?.emptyTextFiles ?? 0,
+            skippedFiles: health?.skippedFiles ?? 0,
         },
         indexedFiles,
         missingFromIndex,
         staleInIndex,
         emptyTextFiles,
-        skippedByReason: skippedCounts(report.skippedFiles),
+        skippedByReason: health?.skippedByReason ?? {},
         omitted: {
-            indexedFiles: report.indexedFiles.length - indexedFiles.length,
-            missingFromIndex: report.missingFromIndex.length - missingFromIndex.length,
-            staleInIndex: report.staleInIndex.length - staleInIndex.length,
-            emptyTextFiles: report.emptyTextFiles.length - emptyTextFiles.length,
+            indexedFiles: Math.max(0, (manifest?.fileCount ?? 0) - indexedFiles.length),
+            missingFromIndex: Math.max(0, (health?.missingFromIndex ?? 0) - missingFromIndex.length),
+            staleInIndex: Math.max(0, (health?.staleInIndex ?? 0) - staleInIndex.length),
+            emptyTextFiles: Math.max(0, (health?.emptyTextFiles ?? 0) - emptyTextFiles.length),
+        },
+        page: {
+            offset,
+            limit,
+            nextOffset: filePage?.nextOffset ?? null,
         },
     };
 }
-function skippedCounts(skippedFiles) {
-    const counts = new Map();
-    for (const skipped of skippedFiles) {
-        counts.set(skipped.reason, (counts.get(skipped.reason) ?? 0) + 1);
+function sourceCatalogOffset(value) {
+    const offset = value ?? 0;
+    if (!Number.isSafeInteger(offset) || offset < 0) {
+        throw new Error("Source catalog offset must be a non-negative integer.");
+    }
+    return offset;
+}
+function sourceCatalogLimit(value) {
+    const limit = value ?? SOURCE_CATALOG_LIMIT;
+    if (!Number.isSafeInteger(limit) || limit <= 0 || limit > MAX_SOURCE_CATALOG_LIMIT) {
+        throw new Error(`Source catalog limit must be a positive integer no greater than ${MAX_SOURCE_CATALOG_LIMIT}.`);
     }
-    return Object.fromEntries([...counts.entries()].sort(([left], [right]) => left.localeCompare(right)));
+    return limit;
 }
 //# sourceMappingURL=context-resources.js.map

package/dist/context-resources.js.map

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

@@ -9,6 +9,33 @@ export declare const DEFAULT_SKILL_TARGET_DIR = ".ragmir/skills";
 export declare const INDEX_MANIFEST_FILENAME = "index-manifest.json";
 export declare const RAGMIR_PROJECT_ROOT_ENV = "RAGMIR_PROJECT_ROOT";
 export declare const VECTOR_DISTANCE_METRIC = "l2";
+export declare const MAX_CONFIGURED_FILE_BYTES = 50000000;
+export declare const MAX_INGEST_CONCURRENCY = 8;
+export declare const MAX_EMBEDDING_BATCH_SIZE = 128;
+export declare const MAX_INGEST_FILE_BATCH_SIZE = 128;
+export declare const MAX_INGEST_SOURCE_WINDOW_BYTES = 50000000;
+export declare const MAX_INGEST_CHUNK_WINDOW = 8192;
+export declare const MAX_INGEST_CHUNKS_PER_FILE = 65536;
+export declare const MAX_INGEST_VECTOR_BYTES_PER_FILE: number;
+export declare const MAX_SEARCH_TOP_K = 100;
+export declare const MAX_HYBRID_TEXT_SCAN_LIMIT = 10000;
+export declare const MAX_CONFIG_ARRAY_ITEMS = 10000;
+export declare const MAX_CONFIG_PATH_CHARACTERS = 4096;
+export declare const MAX_CONFIG_TEXT_CHARACTERS = 2048;
+export declare const MAX_EXTERNAL_COMMAND_ARGUMENTS = 128;
+export declare const MAX_EXTERNAL_COMMAND_TIMEOUT_MS = 900000;
+export declare const MAX_INCLUDE_EXTENSIONS = 128;
+export declare const MAX_MCP_OUTPUT_BYTES = 1048576;
+export declare const MAX_REDACTION_PATTERNS = 64;
+export declare const MAX_REDACTION_PATTERN_CHARACTERS = 2048;
+export declare const MAX_CHUNK_SIZE = 1000000;
+export declare const MAX_WORKLOAD_CONCURRENCY = 16;
+export declare const MAX_WORKLOAD_QUEUE = 1000;
+export declare const MAX_WORKLOAD_QUEUE_TIMEOUT_MS = 900000;
+export declare const DEFAULT_EMBEDDING_MODEL = "intfloat/multilingual-e5-small";
+export declare const DEFAULT_EMBEDDING_MODEL_REVISION = "614241f622f53c4eeff9890bdc4f31cfecc418b3";
+export declare const KNOWN_EMBEDDING_MODEL_REVISIONS: Readonly<Record<string, string>>;
+export declare function defaultEmbeddingModelRevision(model: string): string;
 export declare const RAGMIR_GITIGNORE_ENTRY = ".ragmir/";
 export declare const LEGACY_KB_GITIGNORE_ENTRY = ".kb/";
 export declare const LEGACY_PRIVATE_GITIGNORE_ENTRY = "private/";

package/dist/defaults.d.ts.map

@@ -1 +1 @@
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package/dist/defaults.js

@@ -8,6 +8,38 @@ export const DEFAULT_SKILL_TARGET_DIR = `${RAGMIR_DIR}/skills`;
 export const INDEX_MANIFEST_FILENAME = "index-manifest.json";
 export const RAGMIR_PROJECT_ROOT_ENV = "RAGMIR_PROJECT_ROOT";
 export const VECTOR_DISTANCE_METRIC = "l2";
+export const MAX_CONFIGURED_FILE_BYTES = 50_000_000;
+export const MAX_INGEST_CONCURRENCY = 8;
+export const MAX_EMBEDDING_BATCH_SIZE = 128;
+export const MAX_INGEST_FILE_BATCH_SIZE = 128;
+export const MAX_INGEST_SOURCE_WINDOW_BYTES = 50_000_000;
+export const MAX_INGEST_CHUNK_WINDOW = 8_192;
+export const MAX_INGEST_CHUNKS_PER_FILE = 65_536;
+export const MAX_INGEST_VECTOR_BYTES_PER_FILE = 256 * 1_024 * 1_024;
+export const MAX_SEARCH_TOP_K = 100;
+export const MAX_HYBRID_TEXT_SCAN_LIMIT = 10_000;
+export const MAX_CONFIG_ARRAY_ITEMS = 10_000;
+export const MAX_CONFIG_PATH_CHARACTERS = 4_096;
+export const MAX_CONFIG_TEXT_CHARACTERS = 2_048;
+export const MAX_EXTERNAL_COMMAND_ARGUMENTS = 128;
+export const MAX_EXTERNAL_COMMAND_TIMEOUT_MS = 900_000;
+export const MAX_INCLUDE_EXTENSIONS = 128;
+export const MAX_MCP_OUTPUT_BYTES = 1_048_576;
+export const MAX_REDACTION_PATTERNS = 64;
+export const MAX_REDACTION_PATTERN_CHARACTERS = 2_048;
+export const MAX_CHUNK_SIZE = 1_000_000;
+export const MAX_WORKLOAD_CONCURRENCY = 16;
+export const MAX_WORKLOAD_QUEUE = 1_000;
+export const MAX_WORKLOAD_QUEUE_TIMEOUT_MS = 900_000;
+export const DEFAULT_EMBEDDING_MODEL = "intfloat/multilingual-e5-small";
+export const DEFAULT_EMBEDDING_MODEL_REVISION = "614241f622f53c4eeff9890bdc4f31cfecc418b3";
+export const KNOWN_EMBEDDING_MODEL_REVISIONS = {
+    [DEFAULT_EMBEDDING_MODEL]: DEFAULT_EMBEDDING_MODEL_REVISION,
+    "mixedbread-ai/mxbai-embed-xsmall-v1": "e6ac24e5d6efb8782b59de1647b3ececb4ece94e",
+};
+export function defaultEmbeddingModelRevision(model) {
+    return KNOWN_EMBEDDING_MODEL_REVISIONS[model] ?? "main";
+}
 export const RAGMIR_GITIGNORE_ENTRY = `${RAGMIR_DIR}/`;
 export const LEGACY_KB_GITIGNORE_ENTRY = `${LEGACY_KB_DIR}/`;
 export const LEGACY_PRIVATE_GITIGNORE_ENTRY = `${LEGACY_PRIVATE_DIR}/`;
@@ -24,8 +56,9 @@ export const DEFAULT_CONFIG = {
     embeddingModelPath: `${RAGMIR_DIR}/models`,
     tableName: "chunks",
     embeddingProvider: "local-hash",
-    embeddingModel: "intfloat/multilingual-e5-small",
-    embeddingModelRevision: "main",
+    embeddingModel: DEFAULT_EMBEDDING_MODEL,
+    embeddingModelRevision: DEFAULT_EMBEDDING_MODEL_REVISION,
+    embeddingModelDigest: null,
     transformersAllowRemoteModels: false,
     redaction: {
         enabled: true,
@@ -41,7 +74,14 @@ export const DEFAULT_CONFIG = {
     maxFileBytes: 50_000_000,
     ingestConcurrency: 4,
     embeddingBatchSize: 32,
+    sourceFingerprintMode: "fast",
+    incrementalFailurePolicy: "preserve-last-good",
     hybridTextScanLimit: 5_000,
+    workloadLimits: {
+        search: { concurrency: 8, maxQueue: 64, queueTimeoutMs: 30_000 },
+        embedding: { concurrency: 1, maxQueue: 64, queueTimeoutMs: 30_000 },
+        ingestion: { concurrency: 1, maxQueue: 4, queueTimeoutMs: 120_000 },
+    },
     includeExtensions: [],
     pdfOcrCommand: [],
     pdfOcrTimeoutMs: 120_000,

package/dist/defaults.js.map

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package/dist/destroy.d.ts

@@ -1,3 +1,3 @@
-import type { DestroyIndexResult } from "./types.js";
-export declare function destroyIndex(cwd?: string): Promise<DestroyIndexResult>;
+import type { DestroyIndexResult, OperationOptions } from "./types.js";
+export declare function destroyIndex(cwd?: string, options?: OperationOptions): Promise<DestroyIndexResult>;
 //# sourceMappingURL=destroy.d.ts.map

package/dist/destroy.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"destroy.d.ts","sourceRoot":"","sources":["../src/destroy.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAA;AAEtE,wBAAsB,YAAY,CAChC,GAAG,SAAgB,EACnB,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,kBAAkB,CAAC,CAkC7B"}

package/dist/destroy.js

@@ -6,24 +6,43 @@ import { recordAccess } from "./access-log.js";
 import { loadConfig } from "./config.js";
 import { INDEX_MANIFEST_FILENAME } from "./defaults.js";
 import { disposeTransformersCache } from "./embeddings.js";
+import { withIndexWriteLock } from "./index-write-lock.js";
 import { readIngestionState } from "./ingestion-state.js";
-export async function destroyIndex(cwd = process.cwd()) {
+import { operationSignal } from "./operation.js";
+import { SOURCE_FINGERPRINT_CACHE_FILENAME } from "./source-fingerprint-cache.js";
+export async function destroyIndex(cwd = process.cwd(), options = {}) {
     const config = await loadConfig(cwd);
-    const existed = existsSync(config.storageDir);
-    const hasIngestionState = existed && (await readIngestionState(config)) !== null;
-    await assertSafeIndexStorage(config.projectRoot, config.storageDir, existed, hasIngestionState);
-    await recordAccess(config, { action: "destroy-index" });
-    await rm(config.storageDir, { recursive: true, force: true });
-    // Release any cached Transformers.js pipelines so a subsequent re-ingest with
-    // a different embedding config does not pin stale ONNX weights in memory.
-    await disposeTransformersCache();
-    return {
-        storageDir: config.storageDir,
-        removed: existed,
-        note: "Generated index removed. For forensic deletion guarantees, keep .ragmir/ on an encrypted volume and rotate/destroy the volume key.",
-    };
+    const existedBeforeLock = existsSync(config.storageDir);
+    const signal = operationSignal(options);
+    await assertSafeIndexStoragePath(config.projectRoot, config.storageDir, existedBeforeLock);
+    return withIndexWriteLock(config.storageDir, signal, async () => {
+        const hasIngestionState = (await readIngestionState(config)) !== null;
+        const hasManifest = existsSync(path.join(config.storageDir, INDEX_MANIFEST_FILENAME));
+        const hasFingerprintCache = existsSync(path.join(config.storageDir, SOURCE_FINGERPRINT_CACHE_FILENAME));
+        const existed = existedBeforeLock || hasIngestionState || hasManifest || hasFingerprintCache;
+        await assertSafeIndexStorage(config.projectRoot, config.storageDir, existed, hasIngestionState, hasFingerprintCache);
+        await recordAccess(config, { action: "destroy-index" });
+        await rm(config.storageDir, { recursive: true, force: true });
+        // Release any cached Transformers.js pipelines so a subsequent re-ingest with
+        // a different embedding config does not pin stale ONNX weights in memory.
+        await disposeTransformersCache();
+        return {
+            storageDir: config.storageDir,
+            removed: existed,
+            note: "Generated index removed. For forensic deletion guarantees, keep .ragmir/ on an encrypted volume and rotate/destroy the volume key.",
+        };
+    });
 }
-async function assertSafeIndexStorage(projectRoot, storageDir, existed, hasIngestionState) {
+async function assertSafeIndexStorage(projectRoot, storageDir, existed, hasIngestionState, hasFingerprintCache) {
+    await assertSafeIndexStoragePath(projectRoot, storageDir, existed);
+    if (existed &&
+        !hasIngestionState &&
+        !hasFingerprintCache &&
+        !existsSync(path.join(storageDir, INDEX_MANIFEST_FILENAME))) {
+        throw new Error(`Refusing to remove ${JSON.stringify(storageDir)} because it contains neither ${INDEX_MANIFEST_FILENAME} nor a valid ingestion state.`);
+    }
+}
+async function assertSafeIndexStoragePath(projectRoot, storageDir, existed) {
     const resolvedProjectRoot = await realpath(projectRoot);
     const resolvedStorageDir = existed ? await realpath(storageDir) : path.resolve(storageDir);
     const filesystemRoot = path.parse(resolvedStorageDir).root;
@@ -33,11 +52,6 @@ async function assertSafeIndexStorage(projectRoot, storageDir, existed, hasInges
         isSameOrAncestor(resolvedStorageDir, homeDir)) {
         throw new Error(`Refusing to remove unsafe storageDir ${JSON.stringify(storageDir)}. Configure a dedicated Ragmir index directory.`);
     }
-    if (existed &&
-        !hasIngestionState &&
-        !existsSync(path.join(resolvedStorageDir, INDEX_MANIFEST_FILENAME))) {
-        throw new Error(`Refusing to remove ${JSON.stringify(storageDir)} because it contains neither ${INDEX_MANIFEST_FILENAME} nor a valid ingestion state.`);
-    }
 }
 function isSameOrAncestor(candidate, target) {
     const relative = path.relative(candidate, target);

package/dist/destroy.js.map

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+{"version":3,"file":"destroy.js","sourceRoot":"","sources":["../src/destroy.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,SAAS,CAAA;AACpC,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,MAAM,SAAS,CAAA;AACxB,OAAO,IAAI,MAAM,WAAW,CAAA;AAC5B,OAAO,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAA;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AACxC,OAAO,EAAE,uBAAuB,EAAE,MAAM,eAAe,CAAA;AACvD,OAAO,EAAE,wBAAwB,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAA;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAA;AAChD,OAAO,EAAE,iCAAiC,EAAE,MAAM,+BAA+B,CAAA;AAGjF,MAAM,CAAC,KAAK,UAAU,YAAY,CAChC,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,EACnB,UAA4B,EAAE;IAE9B,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,iBAAiB,GAAG,UAAU,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvD,MAAM,MAAM,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;IACvC,MAAM,0BAA0B,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,UAAU,EAAE,iBAAiB,CAAC,CAAA;IAE1F,OAAO,kBAAkB,CAAC,MAAM,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,IAAI,EAAE;QAC9D,MAAM,iBAAiB,GAAG,CAAC,MAAM,kBAAkB,CAAC,MAAM,CAAC,CAAC,KAAK,IAAI,CAAA;QACrE,MAAM,WAAW,GAAG,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,uBAAuB,CAAC,CAAC,CAAA;QACrF,MAAM,mBAAmB,GAAG,UAAU,CACpC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,iCAAiC,CAAC,CAChE,CAAA;QACD,MAAM,OAAO,GAAG,iBAAiB,IAAI,iBAAiB,IAAI,WAAW,IAAI,mBAAmB,CAAA;QAE5F,MAAM,sBAAsB,CAC1B,MAAM,CAAC,WAAW,EAClB,MAAM,CAAC,UAAU,EACjB,OAAO,EACP,iBAAiB,EACjB,mBAAmB,CACpB,CAAA;QAED,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,eAAe,EAAE,CAAC,CAAA;QACvD,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAA;QAC7D,8EAA8E;QAC9E,0EAA0E;QAC1E,MAAM,wBAAwB,EAAE,CAAA;QAEhC,OAAO;YACL,UAAU,EAAE,MAAM,CAAC,UAAU;YAC7B,OAAO,EAAE,OAAO;YAChB,IAAI,EAAE,oIAAoI;SAC3I,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,KAAK,UAAU,sBAAsB,CACnC,WAAmB,EACnB,UAAkB,EAClB,OAAgB,EAChB,iBAA0B,EAC1B,mBAA4B;IAE5B,MAAM,0BAA0B,CAAC,WAAW,EAAE,UAAU,EAAE,OAAO,CAAC,CAAA;IAElE,IACE,OAAO;QACP,CAAC,iBAAiB;QAClB,CAAC,mBAAmB;QACpB,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,uBAAuB,CAAC,CAAC,EAC3D,CAAC;QACD,MAAM,IAAI,KAAK,CACb,sBAAsB,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,gCAAgC,uBAAuB,+BAA+B,CACvI,CAAA;IACH,CAAC;AACH,CAAC;AAED,KAAK,UAAU,0BAA0B,CACvC,WAAmB,EACnB,UAAkB,EAClB,OAAgB;IAEhB,MAAM,mBAAmB,GAAG,MAAM,QAAQ,CAAC,WAAW,CAAC,CAAA;IACvD,MAAM,kBAAkB,GAAG,OAAO,CAAC,CAAC,CAAC,MAAM,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;IAC1F,MAAM,cAAc,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,IAAI,CAAA;IAC1D,MAAM,OAAO,GAAG,MAAM,QAAQ,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,CAAA;IAE5C,IACE,kBAAkB,KAAK,cAAc;QACrC,gBAAgB,CAAC,kBAAkB,EAAE,mBAAmB,CAAC;QACzD,gBAAgB,CAAC,kBAAkB,EAAE,OAAO,CAAC,EAC7C,CAAC;QACD,MAAM,IAAI,KAAK,CACb,wCAAwC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,iDAAiD,CACpH,CAAA;IACH,CAAC;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,SAAiB,EAAE,MAAc;IACzD,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC,CAAA;IACjD,OAAO,QAAQ,KAAK,EAAE,IAAI,CAAC,CAAC,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAA;AACtF,CAAC"}

package/dist/doctor.d.ts

@@ -1,3 +1,4 @@
-import type { DoctorReport, OperationOptions } from "./types.js";
-export declare function doctor(cwd?: string, options?: OperationOptions): Promise<DoctorReport>;
+import type { Config, DoctorOptions, DoctorReport } from "./types.js";
+export declare function doctor(cwd?: string, options?: DoctorOptions): Promise<DoctorReport>;
+export declare function doctorWithConfig(config: Config, options?: DoctorOptions): Promise<DoctorReport>;
 //# sourceMappingURL=doctor.d.ts.map

package/dist/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AAkBA,OAAO,KAAK,EAAE,YAAY,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAA;AAEhE,wBAAsB,MAAM,CAC1B,GAAG,SAAgB,EACnB,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,YAAY,CAAC,CAuGvB"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AAoBA,OAAO,KAAK,EAAE,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,YAAY,CAAA;AAErE,wBAAsB,MAAM,CAC1B,GAAG,SAAgB,EACnB,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CAKvB;AAED,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CAsIvB"}

package/dist/doctor.js

@@ -3,61 +3,95 @@ import path from "node:path";
 import { findProjectConfig, loadConfig } from "./config.js";
 import { RAGMIR_DIR } from "./defaults.js";
 import { countSkippedByReason } from "./files.js";
-import { getIndexFreshnessWarning, getLexicalScanWarning } from "./index-diagnostics.js";
-import { audit } from "./ingest.js";
+import { getLexicalScanWarning, indexFreshnessWarning } from "./index-diagnostics.js";
+import { auditWithConfig } from "./ingest.js";
 import { operationSignal, throwIfAborted } from "./operation.js";
 import { RGR_RUNNER_FILENAME, rgrCommand } from "./package-manager.js";
-import { securityAudit } from "./security.js";
+import { isCompatibleQualityReport } from "./quality-report.js";
+import { runtimeInfo } from "./runtime-info.js";
+import { securityAuditWithConfig } from "./security.js";
 import { AGENT_HELPER_CONFIG_FILENAMES, AGENT_SETUP_FILENAME, inspectAgentIntegration, MCP_CONFIG_FILENAME, SKILL_NAMES, } from "./skill.js";
-import { countRows, readIndexManifest } from "./store.js";
+import { readIndexManifest, readIndexManifestHeader } from "./store.js";
 export async function doctor(cwd = process.cwd(), options = {}) {
     const signal = operationSignal(options);
     throwIfAborted(signal);
-    const projectConfig = findProjectConfig(cwd);
-    const initialized = existsSync(projectConfig.configPath);
     const config = await loadConfig(cwd);
+    return doctorWithConfig(config, options);
+}
+export async function doctorWithConfig(config, options = {}) {
+    const signal = operationSignal(options);
+    throwIfAborted(signal);
+    const projectConfig = findProjectConfig(config.projectRoot);
+    const initialized = existsSync(projectConfig.configPath);
     throwIfAborted(signal);
     const command = await rgrCommand(config.projectRoot, []);
     throwIfAborted(signal);
     const agentKitInstalled = isAgentKitInstalled(config.projectRoot);
     const agentIntegration = inspectAgentIntegration(config.projectRoot);
     const operationOptions = signal ? { signal } : {};
-    const [auditReport, securityReport, chunksIndexed, manifest, freshnessWarning] = await Promise.all([
-        audit(config.projectRoot, operationOptions),
-        securityAudit(config.projectRoot, operationOptions),
-        countRows(config),
-        readIndexManifest(config),
-        getIndexFreshnessWarning(config),
-    ]);
+    const deep = options.deep === true;
+    const [auditReport, securityReport, manifest] = deep
+        ? await Promise.all([
+            auditWithConfig(config, operationOptions),
+            securityAuditWithConfig(config, operationOptions),
+            readIndexManifest(config),
+        ])
+        : [null, null, await readIndexManifestHeader(config)];
     throwIfAborted(signal);
+    const health = manifest?.health;
+    const supportedFiles = auditReport?.supportedFiles.length ?? health?.supportedFiles ?? 0;
+    const supportedBytes = auditReport?.supportedBytes ?? health?.supportedBytes ?? 0;
+    const largestFileBytes = auditReport?.largestFileBytes ?? health?.largestFileBytes ?? 0;
+    const skippedFiles = auditReport?.skippedFiles.length ?? health?.skippedFiles ?? 0;
+    const unsupportedFiles = auditReport
+        ? countSkippedByReason(auditReport.skippedFiles, "unsupported-extension")
+        : (health?.unsupportedFiles ?? 0);
+    const oversizedFiles = auditReport
+        ? countSkippedByReason(auditReport.skippedFiles, "oversized")
+        : (health?.oversizedFiles ?? 0);
+    const sensitiveFiles = auditReport
+        ? countSkippedByReason(auditReport.skippedFiles, "sensitive-name")
+        : (health?.sensitiveFiles ?? 0);
+    const emptyTextFiles = auditReport?.emptyTextFiles.length ?? health?.emptyTextFiles ?? 0;
+    const indexedFiles = auditReport?.indexedFiles.length ?? manifest?.fileCount ?? 0;
+    const chunksIndexed = auditReport?.totalChunks ?? manifest?.chunkCount ?? 0;
+    const missingFromIndex = auditReport?.missingFromIndex.length ?? health?.missingFromIndex ?? 0;
+    const staleInIndex = auditReport?.staleInIndex.length ?? health?.staleInIndex ?? 0;
+    const securityWarnings = securityReport?.warnings ?? health?.securityWarnings ?? [];
+    const freshnessWarning = indexFreshnessWarning(config, manifest);
     const lexicalScanWarning = chunksIndexed > 0 ? getLexicalScanWarning(config, chunksIndexed) : null;
     const indexFreshness = {
         manifestFound: manifest !== null,
         warning: freshnessWarning,
     };
-    const oversizedFiles = countSkippedByReason(auditReport.skippedFiles, "oversized");
-    const sensitiveFiles = countSkippedByReason(auditReport.skippedFiles, "sensitive-name");
-    const coverageComplete = auditReport.missingFromIndex.length === 0 &&
-        auditReport.staleInIndex.length === 0 &&
-        auditReport.emptyTextFiles.length === 0 &&
+    const diagnosticSnapshotAvailable = deep || health !== undefined;
+    const coverageComplete = diagnosticSnapshotAvailable &&
+        missingFromIndex === 0 &&
+        staleInIndex === 0 &&
+        emptyTextFiles === 0 &&
         oversizedFiles === 0;
-    const operationalReady = initialized && chunksIndexed > 0 && coverageComplete;
-    const indexPolicyCurrent = freshnessWarning === null;
-    const privacyCompliant = securityReport.warnings.length === 0;
+    const operationalReady = initialized && manifest !== null && chunksIndexed > 0 && coverageComplete;
+    const indexPolicyCurrent = manifest !== null && freshnessWarning === null;
+    const privacyCompliant = diagnosticSnapshotAvailable && securityWarnings.length === 0;
+    const retrievalQualityVerified = deep
+        ? await isCompatibleQualityReport(manifest?.qualityReport, manifest, config)
+        : false;
+    throwIfAborted(signal);
     const nextSteps = nextActions({
         initialized,
-        supportedFiles: auditReport.supportedFiles.length,
-        supportedBytes: auditReport.supportedBytes,
-        largestFileBytes: auditReport.largestFileBytes,
-        skippedFiles: auditReport.skippedFiles.length,
-        unsupportedFiles: countSkippedByReason(auditReport.skippedFiles, "unsupported-extension"),
+        diagnosticSnapshotAvailable,
+        supportedFiles,
+        supportedBytes,
+        largestFileBytes,
+        skippedFiles,
+        unsupportedFiles,
         chunksIndexed,
-        missingFromIndex: auditReport.missingFromIndex.length,
-        staleInIndex: auditReport.staleInIndex.length,
-        emptyTextFiles: auditReport.emptyTextFiles.length,
+        missingFromIndex,
+        staleInIndex,
+        emptyTextFiles,
         oversizedFiles,
         sensitiveFiles,
-        warnings: securityReport.warnings.length,
+        warnings: securityWarnings.length,
         embeddingProvider: config.embeddingProvider,
         agentKitInstalled,
         agentRunnerReady: agentIntegration.runnerReady,
@@ -68,10 +102,15 @@ export async function doctor(cwd = process.cwd(), options = {}) {
     });
     throwIfAborted(signal);
     return {
+        mode: deep ? "deep" : "manifest",
+        inventoryVerified: deep,
+        securityVerified: deep,
+        cost: deep ? "O(corpus)" : "O(1)",
         projectRoot: config.projectRoot,
         initialized,
         packageManager: command.packageManager,
         runCommand: command.display,
+        runtime: runtimeInfo(),
         agentKitInstalled,
         agentIntegration,
         rawDir: config.rawDir,
@@ -82,20 +121,21 @@ export async function doctor(cwd = process.cwd(), options = {}) {
         accessLog: config.accessLog,
         privacyProfile: config.privacyProfile,
         retrievalProfile: config.retrievalProfile,
-        supportedFiles: auditReport.supportedFiles.length,
-        supportedBytes: auditReport.supportedBytes,
-        largestFileBytes: auditReport.largestFileBytes,
+        supportedFiles,
+        supportedBytes,
+        largestFileBytes,
         maxFileBytes: config.maxFileBytes,
-        skippedFiles: auditReport.skippedFiles.length,
-        unsupportedFiles: countSkippedByReason(auditReport.skippedFiles, "unsupported-extension"),
+        skippedFiles,
+        unsupportedFiles,
         oversizedFiles,
         sensitiveFiles,
-        emptyTextFiles: auditReport.emptyTextFiles.length,
-        indexedFiles: auditReport.indexedFiles.length,
+        emptyTextFiles,
+        indexedFiles,
         chunksIndexed,
-        missingFromIndex: auditReport.missingFromIndex.length,
-        staleInIndex: auditReport.staleInIndex.length,
-        securityWarnings: securityReport.warnings,
+        missingFromIndex,
+        staleInIndex,
+        corpusFingerprint: manifest?.corpusFingerprint ?? null,
+        securityWarnings,
         indexFreshness,
         ready: operationalReady && indexPolicyCurrent && privacyCompliant,
         readiness: {
@@ -103,7 +143,7 @@ export async function doctor(cwd = process.cwd(), options = {}) {
             coverageComplete,
             indexPolicyCurrent,
             privacyCompliant,
-            retrievalQualityVerified: false,
+            retrievalQualityVerified,
             acceptedRisks: config.acceptedRisks,
         },
         nextSteps,
@@ -115,6 +155,11 @@ function nextActions(input) {
         steps.push(`Run \`${input.run(["setup"])}\` to initialize Ragmir and install the agent kit.`);
         return steps;
     }
+    if (!input.diagnosticSnapshotAvailable) {
+        steps.push(`Run \`${input.run(["doctor", "--deep"])}\` for an O(corpus) source and security audit.`);
+        steps.push(`Run \`${input.run(["ingest"])}\` to create a current manifest before relying on status or search.`);
+        return steps;
+    }
     if (input.supportedFiles === 0) {
         if (input.skippedFiles > 0) {
             steps.push("Ragmir found files, but none are currently indexable. Run `rgr audit --unsupported` to inspect skipped files.");