@jcode.labs/ragmir 2.7.0 → 2.8.0

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

@@ -1 +1 @@
-{"version":3,"file":"access-log.d.ts","sourceRoot":"","sources":["../src/access-log.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EACV,eAAe,EACf,qBAAqB,EACrB,oBAAoB,EACpB,MAAM,EACP,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;AA6BD,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAYvF;AA2BD,wBAAsB,oBAAoB,CACxC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,oBAAoB,CAAC,CAuD/B"}
+{"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,EACP,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;AAmCD,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAgBvF;AA2BD,wBAAsB,oBAAoB,CACxC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,oBAAoB,CAAC,CA2D/B"}

package/dist/access-log.js

@@ -1,8 +1,9 @@
-import { createHash } from "node:crypto";
+import { createHmac, randomBytes } from "node:crypto";
 import { existsSync } from "node:fs";
-import { appendFile, mkdir, readFile, stat, writeFile } from "node:fs/promises";
+import { appendFile, readFile, stat, writeFile } from "node:fs/promises";
 import path from "node:path";
 import { loadConfig } from "./config.js";
+import { ensurePrivateDirectory, hardenPrivateFile } from "./permissions.js";
 const ACCESS_LOG_ACTIONS = [
     "ingest",
     "search",
@@ -22,14 +23,19 @@ const MILLISECONDS_PER_DAY = 24 * 60 * 60 * 1000;
 const MAX_ACCESS_LOG_BYTES = 10 * 1024 * 1024;
 /** Number of most recent lines retained when the log exceeds the byte cap. */
 const TRIMMED_ACCESS_LOG_LINES = 50_000;
+const ACCESS_LOG_SALT_FILE = ".ragmir-access-log.salt";
 export async function recordAccess(config, event) {
     if (!config.accessLog) {
         return;
     }
     try {
-        await mkdir(path.dirname(config.accessLogPath), { recursive: true });
+        await ensurePrivateDirectory(path.dirname(config.accessLogPath));
         await trimAccessLogIfNeeded(config.accessLogPath);
-        await appendFile(config.accessLogPath, `${JSON.stringify(toLogLine(event))}\n`, "utf8");
+        await appendFile(config.accessLogPath, `${JSON.stringify(await toLogLine(config, event))}\n`, {
+            encoding: "utf8",
+            mode: 0o600,
+        });
+        await hardenPrivateFile(config.accessLogPath);
     }
     catch {
         // Access logging is best-effort so read-only workspaces do not block local use.
@@ -64,6 +70,7 @@ export async function accessLogUsageReport(options = {}) {
     const since = new Date(until.getTime() - days * MILLISECONDS_PER_DAY);
     const eventsByAction = emptyEventsByAction();
     const queryHashes = new Set();
+    const resultCountsByAction = emptyResultCountsByAction();
     let totalEvents = 0;
     let invalidLines = 0;
     let resultCountTotal = 0;
@@ -91,6 +98,8 @@ export async function accessLogUsageReport(options = {}) {
             if (typeof event.resultCount === "number") {
                 resultCountTotal += event.resultCount;
                 resultCountEvents += 1;
+                resultCountsByAction[event.action].total += event.resultCount;
+                resultCountsByAction[event.action].events += 1;
             }
             if (lastEventAt === null || event.timestamp > lastEventAt) {
                 lastEventAt = event.timestamp;
@@ -106,21 +115,69 @@ export async function accessLogUsageReport(options = {}) {
         eventsByAction,
         uniqueQueryHashes: queryHashes.size,
         averageResultCount: resultCountEvents === 0 ? null : resultCountTotal / resultCountEvents,
+        averageResultCountByAction: averageResultCounts(resultCountsByAction),
         lastEventAt,
     };
 }
-function toLogLine(event) {
+function emptyResultCountsByAction() {
+    return {
+        ingest: { total: 0, events: 0 },
+        search: { total: 0, events: 0 },
+        ask: { total: 0, events: 0 },
+        research: { total: 0, events: 0 },
+        evaluate: { total: 0, events: 0 },
+        "destroy-index": { total: 0, events: 0 },
+    };
+}
+function averageResultCounts(stats) {
+    return {
+        ingest: averageResultCount(stats.ingest),
+        search: averageResultCount(stats.search),
+        ask: averageResultCount(stats.ask),
+        research: averageResultCount(stats.research),
+        evaluate: averageResultCount(stats.evaluate),
+        "destroy-index": averageResultCount(stats["destroy-index"]),
+    };
+}
+function averageResultCount(stats) {
+    return stats.events === 0 ? null : stats.total / stats.events;
+}
+async function toLogLine(config, event) {
     return {
         timestamp: new Date().toISOString(),
         action: event.action,
-        queryHash: event.query ? hashQuery(event.query) : undefined,
+        queryHash: event.query ? await hashQuery(config, event.query) : undefined,
         topK: event.topK,
         resultCount: event.resultCount,
         redactions: event.redactions,
     };
 }
-function hashQuery(query) {
-    return createHash("sha256").update(query).digest("hex");
+async function hashQuery(config, query) {
+    const salt = await accessLogSalt(config);
+    return createHmac("sha256", salt).update(query).digest("hex");
+}
+async function accessLogSalt(config) {
+    const saltPath = path.join(path.dirname(config.accessLogPath), ACCESS_LOG_SALT_FILE);
+    try {
+        return await readFile(saltPath);
+    }
+    catch (error) {
+        if (!isNodeError(error) || error.code !== "ENOENT") {
+            throw error;
+        }
+    }
+    const salt = randomBytes(32);
+    try {
+        await writeFile(saltPath, salt, { flag: "wx", mode: 0o600 });
+        await hardenPrivateFile(saltPath);
+        return salt;
+    }
+    catch (error) {
+        if (isNodeError(error) && error.code === "EEXIST") {
+            return readFile(saltPath);
+        }
+        throw error;
+    }
 }
 function emptyEventsByAction() {
     return {

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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;AAM3D,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,cAAc,EACxB,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,GACnB,SAAS,EAAE,CA0Cb"}
+{"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"}

package/dist/chunking.js

@@ -1,7 +1,9 @@
 import { createHash } from "node:crypto";
 const PARAGRAPH_BREAK_MIN_RATIO = 0.45;
 const SENTENCE_BREAK_MIN_RATIO = 0.55;
+const LINE_BREAK_MIN_RATIO = 0.65;
 const WHITESPACE_BREAK_MIN_RATIO = 0.75;
+const SENTENCE_BOUNDARIES = [". ", "? ", "! ", "。", "？", "！"];
 export function chunkDocument(document, chunkSize, chunkOverlap) {
     if (!document.text) {
         return [];
@@ -27,6 +29,7 @@ export function chunkDocument(document, chunkSize, chunkOverlap) {
                 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,
@@ -40,6 +43,15 @@ export function chunkDocument(document, chunkSize, chunkOverlap) {
     }
     return chunks;
 }
+function pageRangeForSpan(document, start, end) {
+    if (!document.pages || document.pages.length === 0) {
+        return {};
+    }
+    const overlapping = document.pages.filter((page) => page.charStart < end && page.charEnd > start);
+    const first = overlapping[0];
+    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) {
@@ -50,9 +62,13 @@ function chooseChunkEnd(text, cursor, chunkSize) {
     if (paragraphBreak > chunkSize * PARAGRAPH_BREAK_MIN_RATIO) {
         return cursor + paragraphBreak;
     }
-    const sentenceBreak = Math.max(window.lastIndexOf(". "), window.lastIndexOf("? "), window.lastIndexOf("! "));
-    if (sentenceBreak > chunkSize * SENTENCE_BREAK_MIN_RATIO) {
-        return cursor + sentenceBreak + 1;
+    const sentenceBreakEnd = lastSentenceBreakEnd(window);
+    if (sentenceBreakEnd > chunkSize * SENTENCE_BREAK_MIN_RATIO) {
+        return cursor + sentenceBreakEnd;
+    }
+    const lineBreak = window.lastIndexOf("\n");
+    if (lineBreak > chunkSize * LINE_BREAK_MIN_RATIO) {
+        return cursor + lineBreak;
     }
     const whitespace = window.lastIndexOf(" ");
     if (whitespace > chunkSize * WHITESPACE_BREAK_MIN_RATIO) {
@@ -60,6 +76,16 @@ function chooseChunkEnd(text, cursor, chunkSize) {
     }
     return hardEnd;
 }
+function lastSentenceBreakEnd(text) {
+    let end = -1;
+    for (const boundary of SENTENCE_BOUNDARIES) {
+        const index = text.lastIndexOf(boundary);
+        if (index >= 0) {
+            end = Math.max(end, index + (boundary.endsWith(" ") ? boundary.length - 1 : boundary.length));
+        }
+    }
+    return end;
+}
 function trimmedSpan(text, start, end) {
     let trimmedStart = start;
     let trimmedEnd = end;

package/dist/chunking.js.map

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

@@ -14,6 +14,7 @@ import { countSkippedByReason } from "./files.js";
 import { getIndexFreshnessWarning, getLexicalScanWarning } from "./index-diagnostics.js";
 import { audit, ingest } from "./ingest.js";
 import { initProject } from "./init.js";
+import { ingestionLimits } from "./limits.js";
 import { serveMcp } from "./mcp.js";
 import { rgrCommand } from "./package-manager.js";
 import { routePrompt } from "./prompt-routing.js";
@@ -217,7 +218,7 @@ program
         }
         return;
     }
-    console.log(pc.green(`Done. discoveredFiles=${result.discoveredFiles} supportedFiles=${result.supportedFiles} indexedFiles=${result.indexedFiles} rebuiltFiles=${result.rebuiltFiles} reusedFiles=${result.reusedFiles} chunks=${result.chunks} skippedFiles=${result.skippedFiles} unsupportedFiles=${result.unsupportedFiles} oversizedFiles=${result.oversizedFiles} sensitiveFiles=${result.sensitiveFiles} emptyTextFiles=${result.emptyTextFiles.length} redactions=${result.redactions} errors=${result.errors.length}`));
+    console.log(pc.green(`Done. discoveredFiles=${result.discoveredFiles} supportedFiles=${result.supportedFiles} supportedBytes=${result.supportedBytes} largestFileBytes=${result.largestFileBytes} indexedFiles=${result.indexedFiles} rebuiltFiles=${result.rebuiltFiles} reusedFiles=${result.reusedFiles} chunks=${result.chunks} skippedFiles=${result.skippedFiles} unsupportedFiles=${result.unsupportedFiles} oversizedFiles=${result.oversizedFiles} sensitiveFiles=${result.sensitiveFiles} emptyTextFiles=${result.emptyTextFiles.length} redactions=${result.redactions} errors=${result.errors.length}`));
     printUnsupportedSummary(result.unsupportedExtensions);
     printEmptyTextFiles(result.emptyTextFiles);
     if (result.vectorIndexWarning) {
@@ -243,6 +244,8 @@ program
     .argument("<query>", "Search query.")
     .option("-k, --top-k <number>", "Number of passages to return.", parsePositiveInt)
     .option("--context-radius <number>", "Include neighboring chunks around each matched passage.", parseNonNegativeInt)
+    .option("--include-path <prefix>", "Search only indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
+    .option("--exclude-path <prefix>", "Exclude indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
     .option("--compact", "Return short snippets instead of full passages.")
     .option("--json", "Print machine-readable JSON.")
     .action(async (query, options, command) => {
@@ -275,6 +278,8 @@ program
     .argument("<query>", "Question to answer.")
     .option("-k, --top-k <number>", "Number of passages to use.", parsePositiveInt)
     .option("--context-radius <number>", "Include neighboring chunks around each matched passage.", parseNonNegativeInt)
+    .option("--include-path <prefix>", "Use only indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
+    .option("--exclude-path <prefix>", "Exclude indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
     .option("--json", "Print machine-readable JSON.")
     .action(async (query, options, command) => {
     const cwd = projectRoot(command);
@@ -303,6 +308,8 @@ program
     .argument("<query>", "Research question or topic.")
     .option("-k, --top-k <number>", "Maximum number of evidence passages to keep.", parsePositiveInt)
     .option("--no-code", "Skip the lightweight repository code search.")
+    .option("--include-path <prefix>", "Use only indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
+    .option("--exclude-path <prefix>", "Exclude indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
     .option("--compact", "Return snippets instead of full retrieved passages.")
     .option("--json", "Print machine-readable JSON.")
     .action(async (query, options, command) => {
@@ -310,6 +317,7 @@ program
     const researchOptions = { cwd };
     addOption(researchOptions, "topK", options.topK);
     addOption(researchOptions, "includeCode", options.code);
+    addPathFilters(researchOptions, options);
     const report = await research(query, researchOptions);
     const output = options.compact ? compactResearchReport(report) : report;
     if (options.json) {
@@ -367,25 +375,25 @@ program
     };
     addOption(evaluationOptions, "topK", options.topK);
     const result = await evaluateGoldenQueries(evaluationOptions);
-    const minimumRecall = options.failUnder ?? 1;
-    const passed = result.recall >= minimumRecall;
+    const minimumRecall = options.failUnder;
+    const passed = minimumRecall === undefined || result.recall >= minimumRecall;
     if (options.json) {
-        const payload = options.failUnder === undefined ? result : { ...result, minimumRecall, passed };
+        const payload = minimumRecall === undefined ? result : { ...result, minimumRecall, passed };
         console.log(JSON.stringify(payload, null, 2));
         if (!passed) {
             process.exitCode = 1;
         }
         return;
     }
-    const thresholdSummary = options.failUnder === undefined
+    const thresholdSummary = minimumRecall === undefined
         ? ""
         : ` minimumRecall=${minimumRecall.toFixed(3)} passed=${passed}`;
-    console.log(`golden=${result.goldenPath} total=${result.total} hits=${result.hits} misses=${result.misses} recall=${result.recall.toFixed(3)} mrr=${result.meanReciprocalRank.toFixed(3)} ndcg=${result.ndcg.toFixed(3)}${thresholdSummary}`);
+    console.log(`golden=${result.goldenPath} total=${result.total} hits=${result.hits} misses=${result.misses} hitRate=${result.hitRate.toFixed(3)} recall=${result.recall.toFixed(3)} precision=${result.precision.toFixed(3)} mrr=${result.meanReciprocalRank.toFixed(3)} ndcg=${result.ndcg.toFixed(3)} p50Ms=${result.p50LatencyMs.toFixed(1)} p95Ms=${result.p95LatencyMs.toFixed(1)}${thresholdSummary}`);
     for (const testCase of result.cases) {
         const label = testCase.id ? `${testCase.id}: ${testCase.query}` : testCase.query;
         const status = testCase.hit ? pc.green("hit") : pc.red("miss");
         const rank = testCase.bestRank === null ? "n/a" : String(testCase.bestRank);
-        console.log(`${status} rank=${rank} rr=${testCase.reciprocalRank.toFixed(3)} ndcg=${testCase.ndcg.toFixed(3)} topK=${testCase.topK} ${label}`);
+        console.log(`${status} rank=${rank} recall=${testCase.recall.toFixed(3)} precision=${testCase.precision.toFixed(3)} rr=${testCase.reciprocalRank.toFixed(3)} ndcg=${testCase.ndcg.toFixed(3)} latencyMs=${testCase.latencyMs.toFixed(1)} topK=${testCase.topK} ${label}`);
         if (!testCase.hit) {
             const expected = testCase.expectedCitations === undefined
                 ? testCase.expectedPaths
@@ -413,9 +421,14 @@ program
         console.log(JSON.stringify(report, null, 2));
         return;
     }
+    console.log(`discoveredFiles=${report.discoveredFiles}`);
     console.log(`supportedFiles=${report.supportedFiles.length}`);
+    console.log(`supportedBytes=${report.supportedBytes}`);
+    console.log(`largestFileBytes=${report.largestFileBytes}`);
     console.log(`skippedFiles=${report.skippedFiles.length}`);
     console.log(`unsupportedFiles=${countSkippedByReason(report.skippedFiles, "unsupported-extension")}`);
+    console.log(`oversizedFiles=${countSkippedByReason(report.skippedFiles, "oversized")}`);
+    console.log(`sensitiveFiles=${countSkippedByReason(report.skippedFiles, "sensitive-name")}`);
     console.log(`indexedFiles=${report.indexedFiles.length}`);
     console.log(`totalChunks=${report.totalChunks}`);
     console.log(`emptyTextFiles=${report.emptyTextFiles.length}`);
@@ -475,6 +488,33 @@ program
     for (const [action, count] of Object.entries(report.eventsByAction)) {
         console.log(`events.${action}=${count}`);
     }
+    for (const [action, average] of Object.entries(report.averageResultCountByAction)) {
+        console.log(`averageResults.${action}=${average ?? "n/a"}`);
+    }
+});
+program
+    .command("limits")
+    .description("Show active ingestion limits and practical corpus scaling boundaries.")
+    .option("--json", "Print machine-readable JSON.")
+    .action(async (options, command) => {
+    const cwd = projectRoot(command);
+    const report = ingestionLimits(await loadConfig(cwd));
+    if (options.json) {
+        console.log(JSON.stringify(report, null, 2));
+        return;
+    }
+    console.log(`maxFileBytes=${report.maxFileBytes}`);
+    console.log(`maxFiles=${report.maxFiles ?? "unbounded"}`);
+    console.log(`maxCorpusBytes=${report.maxCorpusBytes ?? "unbounded"}`);
+    console.log(`maxPdfPages=${report.maxPdfPages}`);
+    console.log(`maxPdfTextCharacters=${report.maxPdfTextCharacters}`);
+    console.log(`maxOfficeTextEntries=${report.maxOfficeTextEntries}`);
+    console.log(`maxOfficeEntryBytes=${report.maxOfficeEntryBytes}`);
+    console.log(`maxOfficeTotalTextBytes=${report.maxOfficeTotalTextBytes}`);
+    console.log(`maxExternalTextOutputBytes=${report.maxExternalTextOutputBytes}`);
+    for (const note of report.notes) {
+        console.log(`note: ${note}`);
+    }
 });
 program
     .command("status")
@@ -594,16 +634,17 @@ program
 });
 program
     .command("chat")
-    .description("Answer with a local Transformers.js chat model grounded in Ragmir citations.")
+    .description("Answer with a verified local model grounded in Ragmir citations.")
     .argument("[input...]", "Question to answer, or `setup` / `doctor`.")
     .option("-k, --top-k <number>", "Number of passages to retrieve.", parsePositiveInt)
-    .option("--model <id>", "Transformers.js text-generation model ID.")
-    .option("--model-path <path>", "Local model/cache path.")
-    .option("--offline", "Disable remote model loading.")
-    .option("--allow-remote-models", "Explicitly allow remote model downloads while answering.")
+    .option("--profile <profile>", "Local chat profile: lite, fast, or quality.")
+    .option("--thinking <mode>", "Thinking mode: off, standard, or deep.")
+    .option("--model-path <path>", "Local Gemma model root.")
+    .option("--offline", "Require an already verified local model.")
+    .option("--allow-remote-models", "Compatibility flag for explicit chat setup; normal answers stay local.")
+    .option("--verify", "Recompute the full model SHA256 during doctor.")
     .option("--max-new-tokens <number>", "Maximum generated tokens.", parsePositiveInt)
     .option("--context-limit <number>", "Maximum context characters sent to the model.", parsePositiveInt)
-    .option("--dtype <dtype>", "Transformers.js dtype. Default q4.")
     .option("--json", "Print machine-readable JSON.")
     .action(async (input, options, command) => {
     const cwd = projectRoot(command);
@@ -611,17 +652,18 @@ program
     const mode = chatMode(input);
     if (mode === "doctor") {
         const doctorOptions = { cwd };
+        addOption(doctorOptions, "profile", options.profile);
         addOption(doctorOptions, "modelPath", options.modelPath);
+        addOption(doctorOptions, "verifyHash", options.verify);
         const report = await chat.doctor(doctorOptions);
         printMaybeJson(report, options.json);
         return;
     }
     if (mode === "setup") {
         const setupOptions = { cwd };
-        addOption(setupOptions, "model", options.model);
+        addOption(setupOptions, "profile", options.profile);
         addOption(setupOptions, "modelPath", options.modelPath);
-        addOption(setupOptions, "dtype", options.dtype);
-        addOption(setupOptions, "allowRemoteModels", options.offline ? false : undefined);
+        addOption(setupOptions, "allowRemoteModels", options.offline ? false : options.allowRemoteModels);
         const result = await chat.setupChatModel(setupOptions);
         printMaybeJson(result, options.json);
         return;
@@ -638,9 +680,9 @@ program
         question,
         sources: sources.map(toChatSource),
     };
-    addOption(chatOptions, "model", options.model);
+    addOption(chatOptions, "profile", options.profile);
+    addOption(chatOptions, "thinking", options.thinking);
     addOption(chatOptions, "modelPath", options.modelPath);
-    addOption(chatOptions, "dtype", options.dtype);
     addOption(chatOptions, "allowRemoteModels", chatAllowRemoteModels(options));
     addOption(chatOptions, "maxNewTokens", options.maxNewTokens);
     addOption(chatOptions, "contextCharLimit", options.contextLimit);
@@ -653,9 +695,12 @@ program
         return;
     }
     console.log(`\n${result.answer}\n`);
-    if (sources.length > 0) {
+    if (!result.emptyContext && result.citationStatus !== "valid") {
+        console.error(pc.yellow(`Citation status: ${result.citationStatus}. Review the answer against the retrieved passages.`));
+    }
+    if (result.sources.length > 0) {
         console.log(pc.dim("Sources:"));
-        for (const [index, source] of sources.entries()) {
+        for (const [index, source] of result.sources.entries()) {
             console.log(`  [${index + 1}] ${source.relativePath} chunk=${source.chunkIndex}`);
         }
     }
@@ -843,8 +888,17 @@ function withSearchOptions(cwd, options) {
     const result = { cwd };
     addOption(result, "topK", options.topK);
     addOption(result, "contextRadius", options.contextRadius);
+    addPathFilters(result, options);
     return result;
 }
+function addPathFilters(target, options) {
+    if (options.includePath && options.includePath.length > 0) {
+        target.includePaths = options.includePath;
+    }
+    if (options.excludePath && options.excludePath.length > 0) {
+        target.excludePaths = options.excludePath;
+    }
+}
 async function loadChat() {
     const module = await import(CHAT_PACKAGE_NAME);
     if (!isChatModule(module)) {
@@ -929,8 +983,14 @@ function printDoctor(report) {
     console.log(`redactionEnabled=${report.redactionEnabled}`);
     console.log(`accessLog=${report.accessLog}`);
     console.log(`supportedFiles=${report.supportedFiles}`);
+    console.log(`supportedBytes=${report.supportedBytes}`);
+    console.log(`largestFileBytes=${report.largestFileBytes}`);
+    console.log(`maxFileBytes=${report.maxFileBytes}`);
     console.log(`skippedFiles=${report.skippedFiles}`);
     console.log(`unsupportedFiles=${report.unsupportedFiles}`);
+    console.log(`oversizedFiles=${report.oversizedFiles}`);
+    console.log(`sensitiveFiles=${report.sensitiveFiles}`);
+    console.log(`emptyTextFiles=${report.emptyTextFiles}`);
     console.log(`indexedFiles=${report.indexedFiles}`);
     console.log(`chunksIndexed=${report.chunksIndexed}`);
     console.log(`missingFromIndex=${report.missingFromIndex}`);
@@ -954,7 +1014,7 @@ function printResearchReport(report) {
     console.log(`query=${report.query}`);
     console.log(`ready=${report.ready}`);
     console.log(`generatedQueries=${report.generatedQueries.length}`);
-    console.log(`audit.supportedFiles=${report.audit.supportedFiles} audit.indexedFiles=${report.audit.indexedFiles} audit.totalChunks=${report.audit.totalChunks} audit.skippedFiles=${report.audit.skippedFiles} audit.missingFromIndex=${report.audit.missingFromIndex} audit.staleInIndex=${report.audit.staleInIndex}`);
+    console.log(`audit.supportedFiles=${report.audit.supportedFiles} audit.supportedBytes=${report.audit.supportedBytes} audit.largestFileBytes=${report.audit.largestFileBytes} audit.indexedFiles=${report.audit.indexedFiles} audit.totalChunks=${report.audit.totalChunks} audit.skippedFiles=${report.audit.skippedFiles} audit.oversizedFiles=${report.audit.oversizedFiles} audit.missingFromIndex=${report.audit.missingFromIndex} audit.staleInIndex=${report.audit.staleInIndex}`);
     console.log(`securityWarnings=${report.securityWarnings.length}`);
     console.log(`sourceDiagnostics.duplicates=${report.sourceDiagnostics.duplicateCandidates.length} sourceDiagnostics.archives=${report.sourceDiagnostics.archiveCandidates.length} sourceDiagnostics.mirrors=${report.sourceDiagnostics.mirrorCandidates.length}`);
     if (report.sourceDiagnostics.duplicateCandidates.length > 0) {