@jcode.labs/ragmir 2.9.3 → 2.11.0

package/README.md

@@ -55,7 +55,10 @@ npx rgr audit --unsupported
 npx rgr security-audit
 
 # Retrieval
+npx rgr preview --path docs --max-chunks 3
 npx rgr search "deployment decision"
+npx rgr search "deployment decision" --explain
+npx rgr search "deployment decision" --context-path "Operations > Deployment"
 npx rgr ask "What evidence supports the deployment decision?"
 npx rgr research "deployment obligations" --compact
 
@@ -88,8 +91,11 @@ Frequently used exports:
 | Export | Purpose |
 | --- | --- |
 | `setupProject`, `addSourceEntries` | Initialize project state and select files |
+| `discoverKnowledgeBases`, `knowledgeBaseIdentity` | Route root and nested monorepo bases |
+| `getKnowledgeBaseContext`, `getKnowledgeBaseSourceCatalog` | Give agents bounded readiness and source context |
 | `ingest`, `audit` | Build the index and compare it with files on disk |
-| `search`, `ask`, `research` | Retrieve cited passages at different levels of breadth |
+| `previewChunks` | Inspect redacted chunks and distributions without writing storage |
+| `search`, `ask`, `research`, `expandCitation` | Retrieve or expand cited passages |
 | `doctor`, `securityAudit` | Inspect readiness and local privacy posture |
 | `serveMcp` | Start the read-focused local MCP server |
 | `configurePdfOcr`, `inspectPdfOcr` | Configure and inspect local PDF OCR |
@@ -105,8 +111,13 @@ npx rgr doctor
 ```
 
 Ragmir writes helper files for the selected clients and points them at the current project. MCP
-exposes status, search, ask, research, audit, evaluation, usage, and security tools. It does not
-expose index deletion.
+exposes status, search, ask, research, exact citation expansion, audit, evaluation, usage, and
+security tools. Retrieval responses have a global byte ceiling and expose metadata-only output
+metrics. The server does not expose index deletion.
+
+For a monorepo with root and app-specific bases, run `rgr bases --json` before retrieval when scope
+is unclear. The nearest configured base is active, nested MCP helpers get unique names, and every
+helper pins `RAGMIR_PROJECT_ROOT` so clients cannot drift to a sibling index.
 
 ## Retrieval modes
 
@@ -147,7 +158,8 @@ local executable, never a shell string or cloud OCR service.
 - Generated indexes, models, reports, audio, and access logs belong under ignored `.ragmir/` state.
 - Redaction runs before indexing when configured, but it is not a compliance certification.
 - External extractors and model downloads are opt-in system boundaries.
-- MCP retrieval is bounded and access logs contain metadata, not query text or retrieved passages.
+- MCP retrieval is bounded by `mcpMaxOutputBytes`; access logs contain byte metrics, not query text
+  or retrieved passages.
 
 Read [configuration and privacy](https://github.com/jcode-works/jcode-ragmir/blob/main/docs/configuration.md)
 and [security hardening](https://github.com/jcode-works/jcode-ragmir/blob/main/SECURITY-HARDENING.md)

package/dist/access-log.d.ts

@@ -1,4 +1,4 @@
-import type { AccessLogAction, AccessLogUsageOptions, AccessLogUsageReport, Config } from "./types.js";
+import type { AccessLogAction, AccessLogUsageOptions, AccessLogUsageReport, Config, McpOutputTool } from "./types.js";
 export interface AccessLogEvent {
     action: AccessLogAction;
     query?: string;
@@ -6,6 +6,14 @@ export interface AccessLogEvent {
     resultCount?: number;
     redactions?: number;
 }
+export interface McpOutputLogEvent {
+    tool: McpOutputTool;
+    retrievedBytes: number;
+    returnedBytes: number;
+    compacted: boolean;
+    truncated: boolean;
+}
 export declare function recordAccess(config: Config, event: AccessLogEvent): Promise<void>;
+export declare function recordMcpOutput(config: Config, event: McpOutputLogEvent): Promise<void>;
 export declare function accessLogUsageReport(options?: AccessLogUsageOptions): Promise<AccessLogUsageReport>;
 //# sourceMappingURL=access-log.d.ts.map

package/dist/access-log.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"access-log.d.ts","sourceRoot":"","sources":["../src/access-log.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EACV,eAAe,EACf,qBAAqB,EACrB,oBAAoB,EACpB,MAAM,EACN,aAAa,EACd,MAAM,YAAY,CAAA;AAEnB,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,eAAe,CAAA;IACvB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,WAAW,CAAC,EAAE,MAAM,CAAA;IACpB,UAAU,CAAC,EAAE,MAAM,CAAA;CACpB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,aAAa,CAAA;IACnB,cAAc,EAAE,MAAM,CAAA;IACtB,aAAa,EAAE,MAAM,CAAA;IACrB,SAAS,EAAE,OAAO,CAAA;IAClB,SAAS,EAAE,OAAO,CAAA;CACnB;AAsDD,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAgBvF;AAED,wBAAsB,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyB7F;AA2BD,wBAAsB,oBAAoB,CACxC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,oBAAoB,CAAC,CAoF/B"}

package/dist/access-log.js

@@ -13,6 +13,13 @@ const ACCESS_LOG_ACTIONS = [
     "destroy-index",
 ];
 const ACCESS_LOG_ACTION_SET = new Set(ACCESS_LOG_ACTIONS);
+const MCP_OUTPUT_TOOLS = [
+    "ragmir_search",
+    "ragmir_ask",
+    "ragmir_research",
+    "ragmir_expand",
+];
+const MCP_OUTPUT_TOOL_SET = new Set(MCP_OUTPUT_TOOLS);
 const DEFAULT_USAGE_REPORT_DAYS = 7;
 const MILLISECONDS_PER_DAY = 24 * 60 * 60 * 1000;
 /**
@@ -41,6 +48,32 @@ export async function recordAccess(config, event) {
         // Access logging is best-effort so read-only workspaces do not block local use.
     }
 }
+export async function recordMcpOutput(config, event) {
+    if (!config.accessLog) {
+        return;
+    }
+    try {
+        await ensurePrivateDirectory(path.dirname(config.accessLogPath));
+        await trimAccessLogIfNeeded(config.accessLogPath);
+        const line = {
+            timestamp: new Date().toISOString(),
+            kind: "mcp-output",
+            tool: event.tool,
+            retrievedBytes: event.retrievedBytes,
+            returnedBytes: event.returnedBytes,
+            compacted: event.compacted,
+            truncated: event.truncated,
+        };
+        await appendFile(config.accessLogPath, `${JSON.stringify(line)}\n`, {
+            encoding: "utf8",
+            mode: 0o600,
+        });
+        await hardenPrivateFile(config.accessLogPath);
+    }
+    catch {
+        // Output metrics are best-effort and must never block local retrieval.
+    }
+}
 async function trimAccessLogIfNeeded(accessLogPath) {
     let size = 0;
     try {
@@ -75,6 +108,11 @@ export async function accessLogUsageReport(options = {}) {
     let invalidLines = 0;
     let resultCountTotal = 0;
     let resultCountEvents = 0;
+    let mcpOutputResponses = 0;
+    let mcpRetrievedBytes = 0;
+    let mcpReturnedBytes = 0;
+    let compactedResponses = 0;
+    let truncatedResponses = 0;
     let lastEventAt = null;
     if (existsSync(config.accessLogPath)) {
         const lines = (await readFile(config.accessLogPath, "utf8")).split(/\r?\n/u).filter(Boolean);
@@ -91,6 +129,17 @@ export async function accessLogUsageReport(options = {}) {
                 continue;
             }
             totalEvents += 1;
+            if (isMcpOutputLogLine(event)) {
+                mcpOutputResponses += 1;
+                mcpRetrievedBytes += event.retrievedBytes;
+                mcpReturnedBytes += event.returnedBytes;
+                compactedResponses += event.compacted ? 1 : 0;
+                truncatedResponses += event.truncated ? 1 : 0;
+                if (lastEventAt === null || event.timestamp > lastEventAt) {
+                    lastEventAt = event.timestamp;
+                }
+                continue;
+            }
             eventsByAction[event.action] += 1;
             if (event.queryHash) {
                 queryHashes.add(event.queryHash);
@@ -116,6 +165,15 @@ export async function accessLogUsageReport(options = {}) {
         uniqueQueryHashes: queryHashes.size,
         averageResultCount: resultCountEvents === 0 ? null : resultCountTotal / resultCountEvents,
         averageResultCountByAction: averageResultCounts(resultCountsByAction),
+        mcpOutput: {
+            responses: mcpOutputResponses,
+            retrievedBytes: mcpRetrievedBytes,
+            returnedBytes: mcpReturnedBytes,
+            savedBytes: mcpRetrievedBytes - mcpReturnedBytes,
+            reductionRatio: mcpRetrievedBytes === 0 ? null : 1 - mcpReturnedBytes / mcpRetrievedBytes,
+            compactedResponses,
+            truncatedResponses,
+        },
         lastEventAt,
     };
 }
@@ -201,15 +259,29 @@ function normalizeUsageReportDays(days) {
 function parseAccessLogLine(line) {
     try {
         const parsed = JSON.parse(line);
-        if (!isAccessLogLine(parsed)) {
-            return null;
+        if (isAccessLogLine(parsed) || isMcpOutputLogLine(parsed)) {
+            return parsed;
         }
-        return parsed;
+        return null;
     }
     catch {
         return null;
     }
 }
+function isMcpOutputLogLine(value) {
+    return (typeof value === "object" &&
+        value !== null &&
+        hasTimestamp(value) &&
+        "kind" in value &&
+        value.kind === "mcp-output" &&
+        "tool" in value &&
+        typeof value.tool === "string" &&
+        MCP_OUTPUT_TOOL_SET.has(value.tool) &&
+        hasNonNegativeNumber(value, "retrievedBytes") &&
+        hasNonNegativeNumber(value, "returnedBytes") &&
+        hasBoolean(value, "compacted") &&
+        hasBoolean(value, "truncated"));
+}
 function isAccessLogLine(value) {
     return (typeof value === "object" &&
         value !== null &&
@@ -230,4 +302,11 @@ function hasOptionalQueryHash(value) {
 function hasOptionalResultCount(value) {
     return !("resultCount" in value) || typeof value.resultCount === "number";
 }
+function hasNonNegativeNumber(value, key) {
+    const field = Reflect.get(value, key);
+    return typeof field === "number" && Number.isFinite(field) && field >= 0;
+}
+function hasBoolean(value, key) {
+    return typeof Reflect.get(value, key) === "boolean";
+}
 //# sourceMappingURL=access-log.js.map

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package/dist/chunk-stats.d.ts

@@ -0,0 +1,8 @@
+import type { ChunkStats } from "./types.js";
+interface ChunkShape {
+    contextPath: string;
+    text: string;
+}
+export declare function summarizeChunkStats(chunks: readonly ChunkShape[]): ChunkStats;
+export {};
+//# sourceMappingURL=chunk-stats.d.ts.map

package/dist/chunk-stats.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"chunk-stats.d.ts","sourceRoot":"","sources":["../src/chunk-stats.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,YAAY,CAAA;AAE5C,UAAU,UAAU;IAClB,WAAW,EAAE,MAAM,CAAA;IACnB,IAAI,EAAE,MAAM,CAAA;CACb;AAED,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,SAAS,UAAU,EAAE,GAAG,UAAU,CA2B7E"}

package/dist/chunk-stats.js

@@ -0,0 +1,31 @@
+export function summarizeChunkStats(chunks) {
+    if (chunks.length === 0) {
+        return {
+            count: 0,
+            minChars: 0,
+            averageChars: 0,
+            p50Chars: 0,
+            p95Chars: 0,
+            maxChars: 0,
+            contextualChunks: 0,
+            contextualRatio: 0,
+        };
+    }
+    const lengths = chunks.map((chunk) => chunk.text.length).sort((left, right) => left - right);
+    const contextualChunks = chunks.filter((chunk) => chunk.contextPath.trim().length > 0).length;
+    return {
+        count: chunks.length,
+        minChars: lengths[0] ?? 0,
+        averageChars: lengths.reduce((sum, length) => sum + length, 0) / lengths.length,
+        p50Chars: percentile(lengths, 0.5),
+        p95Chars: percentile(lengths, 0.95),
+        maxChars: lengths.at(-1) ?? 0,
+        contextualChunks,
+        contextualRatio: contextualChunks / chunks.length,
+    };
+}
+function percentile(sortedValues, quantile) {
+    const index = Math.ceil(quantile * sortedValues.length) - 1;
+    return sortedValues[Math.max(0, index)] ?? 0;
+}
+//# sourceMappingURL=chunk-stats.js.map

package/dist/chunk-stats.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"chunk-stats.js","sourceRoot":"","sources":["../src/chunk-stats.ts"],"names":[],"mappings":"AAOA,MAAM,UAAU,mBAAmB,CAAC,MAA6B;IAC/D,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO;YACL,KAAK,EAAE,CAAC;YACR,QAAQ,EAAE,CAAC;YACX,YAAY,EAAE,CAAC;YACf,QAAQ,EAAE,CAAC;YACX,QAAQ,EAAE,CAAC;YACX,QAAQ,EAAE,CAAC;YACX,gBAAgB,EAAE,CAAC;YACnB,eAAe,EAAE,CAAC;SACnB,CAAA;IACH,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,IAAI,GAAG,KAAK,CAAC,CAAA;IAC5F,MAAM,gBAAgB,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,MAAM,CAAA;IAE7F,OAAO;QACL,KAAK,EAAE,MAAM,CAAC,MAAM;QACpB,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;QACzB,YAAY,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,GAAG,GAAG,MAAM,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,MAAM;QAC/E,QAAQ,EAAE,UAAU,CAAC,OAAO,EAAE,GAAG,CAAC;QAClC,QAAQ,EAAE,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC;QACnC,QAAQ,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC7B,gBAAgB;QAChB,eAAe,EAAE,gBAAgB,GAAG,MAAM,CAAC,MAAM;KAClD,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,YAAsB,EAAE,QAAgB;IAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;IAC3D,OAAO,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,CAAC,CAAA;AAC9C,CAAC"}

package/dist/chunking.d.ts

@@ -1,3 +1,4 @@
 import type { ParsedDocument, TextChunk } from "./types.js";
 export declare function chunkDocument(document: ParsedDocument, chunkSize: number, chunkOverlap: number): TextChunk[];
+export declare function chunkSearchText(chunk: Pick<TextChunk, "contextPath" | "text">): string;
 //# sourceMappingURL=chunking.d.ts.map

package/dist/chunking.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"chunking.d.ts","sourceRoot":"","sources":["../src/chunking.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AAQ3D,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,cAAc,EACxB,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,GACnB,SAAS,EAAE,CA2Cb"}
+{"version":3,"file":"chunking.d.ts","sourceRoot":"","sources":["../src/chunking.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AAQ3D,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,cAAc,EACxB,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,GACnB,SAAS,EAAE,CA+Db;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,IAAI,CAAC,SAAS,EAAE,aAAa,GAAG,MAAM,CAAC,GAAG,MAAM,CAEtF"}

package/dist/chunking.js

@@ -1,4 +1,5 @@
 import { createHash } from "node:crypto";
+import { markdownFenceSpans, structuralSpans } from "./document-structure.js";
 const PARAGRAPH_BREAK_MIN_RATIO = 0.45;
 const SENTENCE_BREAK_MIN_RATIO = 0.55;
 const LINE_BREAK_MIN_RATIO = 0.65;
@@ -10,39 +11,61 @@ export function chunkDocument(document, chunkSize, chunkOverlap) {
     }
     const chunks = [];
     const lineStarts = lineStartOffsets(document.text);
-    let cursor = 0;
+    const structured = structuralSpans(document.text, document.file.extension, chunkSize);
+    const regions = structured.length > 0
+        ? structured
+        : [
+            {
+                charStart: 0,
+                charEnd: document.text.length,
+                contextPath: "",
+                kind: "markdown-section",
+            },
+        ];
+    const fences = [".md", ".mdx", ".markdown"].includes(document.file.extension)
+        ? markdownFenceSpans(document.text)
+        : [];
     let chunkIndex = 0;
-    while (cursor < document.text.length) {
-        const end = chooseChunkEnd(document.text, cursor, chunkSize);
-        const span = trimmedSpan(document.text, cursor, end);
-        if (span.text) {
-            const id = createHash("sha256")
-                .update(`${document.file.relativePath}:${chunkIndex}:${span.text}`)
-                .digest("hex");
-            chunks.push({
-                id,
-                source: document.file.source,
-                relativePath: document.file.relativePath,
-                chunkIndex,
-                text: span.text,
-                charStart: span.start,
-                charEnd: span.end,
-                lineStart: lineNumberForOffset(lineStarts, span.start),
-                lineEnd: lineNumberForOffset(lineStarts, Math.max(span.start, span.end - 1)),
-                ...pageRangeForSpan(document, span.start, span.end),
-                checksum: document.file.checksum,
-                bytes: document.file.bytes,
-                mtimeMs: document.file.mtimeMs,
-            });
-            chunkIndex += 1;
+    for (const region of regions) {
+        let cursor = region.charStart;
+        while (cursor < region.charEnd) {
+            const end = chooseChunkEnd(document.text, cursor, chunkSize, region.charEnd, fences);
+            const span = trimmedSpan(document.text, cursor, end);
+            if (span.text) {
+                const id = createHash("sha256")
+                    .update(`${document.file.relativePath}:${chunkIndex}:${region.contextPath}:${span.text}`)
+                    .digest("hex");
+                chunks.push({
+                    id,
+                    source: document.file.source,
+                    relativePath: document.file.relativePath,
+                    chunkIndex,
+                    contextPath: region.contextPath,
+                    text: span.text,
+                    charStart: span.start,
+                    charEnd: span.end,
+                    lineStart: lineNumberForOffset(lineStarts, span.start),
+                    lineEnd: lineNumberForOffset(lineStarts, Math.max(span.start, span.end - 1)),
+                    ...pageRangeForSpan(document, span.start, span.end),
+                    checksum: document.file.checksum,
+                    bytes: document.file.bytes,
+                    mtimeMs: document.file.mtimeMs,
+                });
+                chunkIndex += 1;
+            }
+            if (end >= region.charEnd) {
+                break;
+            }
+            cursor = fences.some((fence) => fence.start === end)
+                ? end
+                : Math.max(end - chunkOverlap, cursor + 1, region.charStart);
         }
-        if (end >= document.text.length) {
-            break;
-        }
-        cursor = Math.max(end - chunkOverlap, cursor + 1);
     }
     return chunks;
 }
+export function chunkSearchText(chunk) {
+    return chunk.contextPath ? `${chunk.contextPath}\n${chunk.text}` : chunk.text;
+}
 function pageRangeForSpan(document, start, end) {
     if (!document.pages || document.pages.length === 0) {
         return {};
@@ -52,11 +75,15 @@ function pageRangeForSpan(document, start, end) {
     const last = overlapping.at(-1);
     return first && last ? { pageStart: first.pageNumber, pageEnd: last.pageNumber } : {};
 }
-function chooseChunkEnd(text, cursor, chunkSize) {
-    const hardEnd = Math.min(cursor + chunkSize, text.length);
-    if (hardEnd === text.length) {
+function chooseChunkEnd(text, cursor, chunkSize, regionEnd, fences) {
+    const hardEnd = Math.min(cursor + chunkSize, regionEnd);
+    if (hardEnd === regionEnd) {
         return hardEnd;
     }
+    const intersectedFence = fences.find((fence) => fence.start < hardEnd && fence.end > hardEnd && fence.end <= regionEnd);
+    if (intersectedFence && intersectedFence.end - intersectedFence.start <= chunkSize) {
+        return intersectedFence.start > cursor ? intersectedFence.start : intersectedFence.end;
+    }
     const window = text.slice(cursor, hardEnd);
     const paragraphBreak = window.lastIndexOf("\n\n");
     if (paragraphBreak > chunkSize * PARAGRAPH_BREAK_MIN_RATIO) {

package/dist/chunking.js.map

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