@jcode.labs/ragmir 4.2.2 → 5.0.0

package/dist/cli.js

@@ -2,9 +2,7 @@
 import path from "node:path";
 import { Command } from "commander";
 import pc from "picocolors";
-import { accessLogUsageReport } from "./access-log.js";
-import { audioAllowRemoteModels, audioEngine, audioLanguage, parseAgentInstallMode, parseAgentInstallScope, parseIncrementalFailurePolicy, parseNonNegativeInt, parseNumber, parsePositiveInt, parseRecallThreshold, } from "./cli-options.js";
-import { readBoundedStdin } from "./cli-stdin.js";
+import { parseAgentInstallMode, parseAgentInstallScope, parseIncrementalFailurePolicy, parseNonNegativeInt, parsePositiveInt, parseRecallThreshold, } from "./cli-options.js";
 import { loadConfig } from "./config.js";
 import { DEFAULT_SKILL_TARGET_DIR } from "./defaults.js";
 import { destroyIndex } from "./destroy.js";
@@ -22,11 +20,9 @@ import { ingestionLimits } from "./limits.js";
 import { serveMcp } from "./mcp.js";
 import { configurePdfOcr, extractPdfPage, extractPdfPages, inspectPdfOcr, parsePdfOcrEngine, parsePdfOcrPages, } from "./ocr.js";
 import { rgrCommand } from "./package-manager.js";
-import { exportPortableKnowledgeBase, verifyPortableKnowledgeBase } from "./portable.js";
 import { previewChunks } from "./preview.js";
-import { routePrompt } from "./prompt-routing.js";
-import { ask, search } from "./query.js";
-import { compactResearchReport, compactSearchResults, research } from "./research.js";
+import { search } from "./query.js";
+import { compactSearchResults } from "./search-output.js";
 import { securityAudit } from "./security.js";
 import { enableSemanticEmbeddings } from "./semantic-config.js";
 import { setupProject } from "./setup.js";
@@ -34,21 +30,11 @@ import { bundledSkillPath, installAgentSkills, installSkill, parseAgentTargets,
 import { addSourceEntries, listSourceEntries } from "./sources.js";
 import { optimizeStorage } from "./storage-maintenance.js";
 import { readIndexManifestHeader } from "./store.js";
-import { compareTeamSnapshots, createTeamSnapshot, readTeamSnapshot, writeTeamSnapshot, } from "./team-diagnostics.js";
-import { syncTeamKnowledge, } from "./team-sync.js";
 import { inspectUpgrade, upgradeProject } from "./upgrade.js";
 import { VERSION } from "./version.js";
 const SEARCH_TEXT_PREVIEW_LENGTH = 900;
-const CHAT_PACKAGE_NAME = "@jcode.labs/ragmir-chat";
-const TTS_PACKAGE_NAME = "@jcode.labs/ragmir-tts";
-const DEPRECATED_CLI_NAMES = new Set(["ragmir", "kb"]);
 const PUBLIC_CLI_NAME = "rgr";
-const TEAM_DIFF_PREVIEW_LIMIT = 20;
 const program = new Command();
-const deprecatedCliName = deprecatedCliInvocation();
-if (deprecatedCliName !== null) {
-    console.error(pc.yellow(`The \`${deprecatedCliName}\` CLI command is deprecated and will be removed in a future release. Use \`rgr\` instead.`));
-}
 program
     .name(PUBLIC_CLI_NAME)
     .description("Local-first RAG knowledge base for private project documents.")
@@ -175,7 +161,7 @@ ocrCommand
 });
 program
     .command("doctor")
-    .description("Diagnose setup, index freshness, privacy posture, and next steps.")
+    .description("Diagnose setup, index freshness, and next steps.")
     .option("--fix", "Create missing scaffolding, install the agent kit, and rebuild stale indexes.")
     .option("--deep", "Run the O(corpus) source inventory and executable security probes.")
     .option("--json", "Print machine-readable JSON.")
@@ -215,7 +201,6 @@ program
         console.log(`runtimeRagmirVersion=${inspection.runtimeRagmirVersion}`);
         console.log(`indexedWithRagmirVersion=${inspection.indexedWithRagmirVersion ?? "unavailable"}`);
         console.log(`ready=${inspection.ready}`);
-        console.log(`privacyCompliant=${inspection.privacyCompliant}`);
         console.log(`safeActivation=${inspection.safeActivation}`);
         if (inspection.reason) {
             console.log(`reason=${inspection.reason}`);
@@ -237,7 +222,6 @@ program
     console.log(`runtimeRagmirVersion=${result.runtimeRagmirVersion}`);
     console.log(`indexedWithRagmirVersion=${result.indexedWithRagmirVersion ?? "unavailable"}`);
     console.log(`ready=${result.ready}`);
-    console.log(`privacyCompliant=${result.privacyCompliant}`);
     console.log(`safeActivation=${result.safeActivation}`);
     console.log(`action=${result.action}`);
     console.log(`previousIndexedWithRagmirVersion=${result.previousIndexedWithRagmirVersion ?? "unavailable"}`);
@@ -358,7 +342,7 @@ sourcesCommand
 });
 program
     .command("ingest")
-    .description("Parse changed documents, redact, chunk, embed locally, and update LanceDB.")
+    .description("Parse changed documents, chunk, embed locally, and update LanceDB.")
     .option("--rebuild", "Force a full local index rebuild instead of reusing unchanged rows.")
     .option("--batch-size <number>", "Files committed per resumable batch.", parsePositiveInt)
     .option("--incremental-failure-policy <policy>", "Preserve last-good rows after a file failure, or remove stale rows.", parseIncrementalFailurePolicy)
@@ -379,7 +363,7 @@ program
         }
         return;
     }
-    console.log(pc.green(`Done. runId=${result.runId} resumed=${result.resumed} batchSize=${result.batchSize} discoveredFiles=${result.discoveredFiles} supportedFiles=${result.supportedFiles} supportedBytes=${result.supportedBytes} largestFileBytes=${result.largestFileBytes} indexedFiles=${result.indexedFiles} rebuiltFiles=${result.rebuiltFiles} reusedFiles=${result.reusedFiles} staleLastKnownGood=${result.staleLastKnownGood.length} chunks=${result.chunks} skippedFiles=${result.skippedFiles} unsupportedFiles=${result.unsupportedFiles} oversizedFiles=${result.oversizedFiles} sensitiveFiles=${result.sensitiveFiles} emptyTextFiles=${result.emptyTextFiles.length} redactions=${result.redactions} ocrPages=${result.ocr.pages} ocrCacheHits=${result.ocr.cacheHits} ocrBatches=${result.ocr.batches} ocrSubprocesses=${result.ocr.subprocesses} ocrDurationMs=${result.ocr.durationMs} errors=${result.errors.length}`));
+    console.log(pc.green(`Done. runId=${result.runId} resumed=${result.resumed} batchSize=${result.batchSize} discoveredFiles=${result.discoveredFiles} supportedFiles=${result.supportedFiles} supportedBytes=${result.supportedBytes} largestFileBytes=${result.largestFileBytes} indexedFiles=${result.indexedFiles} rebuiltFiles=${result.rebuiltFiles} reusedFiles=${result.reusedFiles} staleLastKnownGood=${result.staleLastKnownGood.length} chunks=${result.chunks} skippedFiles=${result.skippedFiles} unsupportedFiles=${result.unsupportedFiles} oversizedFiles=${result.oversizedFiles} sensitiveFiles=${result.sensitiveFiles} emptyTextFiles=${result.emptyTextFiles.length} ocrPages=${result.ocr.pages} ocrCacheHits=${result.ocr.cacheHits} ocrBatches=${result.ocr.batches} ocrSubprocesses=${result.ocr.subprocesses} ocrDurationMs=${result.ocr.durationMs} errors=${result.errors.length}`));
     printUnsupportedSummary(result.unsupportedExtensions);
     printEmptyTextFiles(result.emptyTextFiles);
     if (result.vectorIndexWarning) {
@@ -404,7 +388,7 @@ program
 });
 program
     .command("preview")
-    .description("Preview redacted chunks and structure without writing the index.")
+    .description("Preview source chunks and structure without writing the index.")
     .option("--path <prefix>", "Preview only source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
     .option("--max-files <number>", "Maximum number of matching files to parse.", parsePositiveInt)
     .option("--max-chunks <number>", "Maximum number of chunks to show per file.", parsePositiveInt)
@@ -434,7 +418,7 @@ program
         console.log(pc.yellow(`unmatched: ${unmatchedPath}`));
     }
     for (const file of report.files) {
-        console.log(`\n${pc.cyan(file.relativePath)} chunks=${file.chunkStats.count} redactions=${file.redactions} minChars=${file.chunkStats.minChars} p50Chars=${file.chunkStats.p50Chars} p95Chars=${file.chunkStats.p95Chars} maxChars=${file.chunkStats.maxChars} contextualRatio=${file.chunkStats.contextualRatio.toFixed(3)}`);
+        console.log(`\n${pc.cyan(file.relativePath)} chunks=${file.chunkStats.count} minChars=${file.chunkStats.minChars} p50Chars=${file.chunkStats.p50Chars} p95Chars=${file.chunkStats.p95Chars} maxChars=${file.chunkStats.maxChars} contextualRatio=${file.chunkStats.contextualRatio.toFixed(3)}`);
         if (file.ocr) {
             console.log(`ocrPages=${file.ocr.pages} ocrCacheHits=${file.ocr.cacheHits} ocrBatches=${file.ocr.batches} ocrSubprocesses=${file.ocr.subprocesses} ocrDurationMs=${file.ocr.durationMs}`);
         }
@@ -497,112 +481,6 @@ program
         }
     }
 });
-program
-    .command("ask")
-    .description("Return cited retrieval context for a question without calling an LLM.")
-    .argument("<query>", "Question to answer.")
-    .option("-k, --top-k <number>", "Number of passages to use.", parsePositiveInt)
-    .option("--max-chunks-per-document <number>", "Maximum primary passages per document before ranked backfill.", parsePositiveInt)
-    .option("--context-radius <number>", "Include neighboring chunks around each matched passage.", parseNonNegativeInt)
-    .option("--include-path <prefix>", "Use only indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
-    .option("--exclude-path <prefix>", "Exclude indexed source paths under this prefix. Repeat for multiple prefixes.", collectOptionValue, [])
-    .option("--context-path <prefix>", "Use only chunks under this structural context. Repeat for multiple prefixes.", collectOptionValue, [])
-    .option("--explain", "Include hybrid score contributions, ranks, and matched terms.")
-    .option("--exact-vector-search", "Bypass ANN and use exhaustive vector search for diagnostics.")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (query, options, command) => {
-    const cwd = projectRoot(command);
-    const result = await ask(query, withSearchOptions(cwd, options));
-    if (options.json) {
-        console.log(JSON.stringify({ query, ...result }, null, 2));
-        if (result.sources.length === 0) {
-            process.exitCode = 1;
-        }
-        return;
-    }
-    console.log(`\n${result.answer}\n`);
-    if (result.staleWarning) {
-        console.error(pc.yellow(result.staleWarning));
-    }
-    if (result.sources.length > 0) {
-        console.log(pc.dim("Sources:"));
-        for (const [index, source] of result.sources.entries()) {
-            const score = source.score ? ` score=${source.score.combinedScore.toFixed(6)}` : "";
-            console.log(`  [${index + 1}] ${source.citation} chunk=${source.chunkIndex}${score}`);
-        }
-    }
-});
-program
-    .command("research")
-    .description("Run a bounded multi-query research pass with cited evidence.")
-    .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("--full-audit", "Run a full source inventory instead of manifest health checks.")
-    .option("--timeout-ms <number>", "Bound the complete research operation.", parsePositiveInt)
-    .option("--code-top-k <number>", "Maximum number of code matches to keep.", parsePositiveInt)
-    .option("--code-scan-max-files <number>", "Maximum code files to read.", parsePositiveInt)
-    .option("--code-scan-max-bytes <number>", "Maximum total code bytes to read.", parsePositiveInt)
-    .option("--code-scan-concurrency <number>", "Maximum concurrent code file reads.", parsePositiveInt)
-    .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("--context-path <prefix>", "Use only chunks under this structural context. 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) => {
-    const cwd = projectRoot(command);
-    const researchOptions = { cwd };
-    addOption(researchOptions, "topK", options.topK);
-    addOption(researchOptions, "includeCode", options.code);
-    addOption(researchOptions, "fullAudit", options.fullAudit);
-    addOption(researchOptions, "timeoutMs", options.timeoutMs);
-    addOption(researchOptions, "codeTopK", options.codeTopK);
-    addOption(researchOptions, "codeScanMaxFiles", options.codeScanMaxFiles);
-    addOption(researchOptions, "codeScanMaxBytes", options.codeScanMaxBytes);
-    addOption(researchOptions, "codeScanConcurrency", options.codeScanConcurrency);
-    addPathFilters(researchOptions, options);
-    const report = await research(query, researchOptions);
-    const output = options.compact ? compactResearchReport(report) : report;
-    if (options.json) {
-        console.log(JSON.stringify(output, null, 2));
-        if (!report.ready) {
-            process.exitCode = 1;
-        }
-        return;
-    }
-    printResearchReport(output);
-    if (!report.ready) {
-        process.exitCode = 1;
-    }
-});
-program
-    .command("route-prompt")
-    .description("Classify a prompt and suggest whether an agent should use Ragmir local context.")
-    .argument("[prompt...]", "Prompt text to classify. Reads stdin when omitted.")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (promptParts, options) => {
-    const prompt = await promptInput(promptParts);
-    if (prompt.trim().length === 0) {
-        console.error(pc.red("Missing prompt. Pass text or pipe it on stdin."));
-        process.exitCode = 1;
-        return;
-    }
-    const decision = routePrompt(prompt);
-    if (options.json) {
-        console.log(JSON.stringify(decision, null, 2));
-        return;
-    }
-    console.log(`shouldUseRagmir=${decision.shouldUseRagmir}`);
-    console.log(`confidence=${decision.confidence.toFixed(2)}`);
-    console.log(`tool=${decision.tool}`);
-    if (decision.query !== null) {
-        console.log(`query=${decision.query}`);
-    }
-    console.log(`reason=${decision.reason}`);
-    if (decision.matchedSignals.length > 0) {
-        console.log(`matchedSignals=${decision.matchedSignals.join(", ")}`);
-    }
-});
 program
     .command("evaluate")
     .description("Measure retrieval quality against a JSON golden query file.")
@@ -724,33 +602,6 @@ program
         process.exitCode = 1;
     }
 });
-program
-    .command("usage-report")
-    .description("Summarize the metadata-only local access log.")
-    .option("--days <number>", "Number of recent days to include.", parsePositiveInt, 7)
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (options, command) => {
-    const cwd = projectRoot(command);
-    const report = await accessLogUsageReport({ cwd, days: options.days });
-    if (options.json) {
-        console.log(JSON.stringify(report, null, 2));
-        return;
-    }
-    console.log(`accessLogEnabled=${report.accessLogEnabled}`);
-    console.log(`since=${report.since}`);
-    console.log(`until=${report.until}`);
-    console.log(`totalEvents=${report.totalEvents}`);
-    console.log(`invalidLines=${report.invalidLines}`);
-    console.log(`uniqueQueryHashes=${report.uniqueQueryHashes}`);
-    console.log(`averageResultCount=${report.averageResultCount ?? "n/a"}`);
-    console.log(`lastEventAt=${report.lastEventAt ?? "n/a"}`);
-    for (const [action, count] of Object.entries(report.eventsByAction)) {
-        console.log(`events.${action}=${count}`);
-    }
-    for (const [action, average] of Object.entries(report.averageResultCountByAction)) {
-        console.log(`averageResults.${action}=${average ?? "n/a"}`);
-    }
-});
 program
     .command("limits")
     .description("Show active ingestion limits and practical corpus scaling boundaries.")
@@ -802,84 +653,6 @@ program
         console.log(`${marker} ${base.id} format=${format} root=${base.projectRoot}`);
     }
 });
-const teamCommand = program
-    .command("team")
-    .description("Synchronize Git-backed team knowledge or inspect advanced index drift.");
-teamCommand
-    .command("sync")
-    .description("Safely fast-forward from Git upstream and refresh the local index.")
-    .option("--no-pull", "Fetch and compare without changing the checked-out branch.")
-    .option("--no-fetch", "Use only the cached upstream reference and local worktree.")
-    .option("--check", "Fetch and report without changing the worktree or index.")
-    .option("--git-timeout-ms <number>", "Bound each Git command.", parsePositiveInt)
-    .option("--json", "Print machine-readable JSON.")
-    .option("--strict", "Exit with code 1 unless Git and the local index are synchronized.")
-    .action(async (options, command) => {
-    const syncOptions = {
-        cwd: projectRoot(command),
-        autoPull: options.pull,
-        fetch: options.fetch,
-        check: options.check === true,
-    };
-    addOption(syncOptions, "gitTimeoutMs", options.gitTimeoutMs);
-    const report = await syncTeamKnowledge(syncOptions);
-    if (options.json) {
-        console.log(JSON.stringify(report, null, 2));
-    }
-    else {
-        printTeamSync(report);
-    }
-    if (options.strict && !report.synchronized) {
-        process.exitCode = 1;
-    }
-});
-teamCommand
-    .command("snapshot")
-    .description("Export relative paths, checksums, configuration, readiness, and corpus identity.")
-    .requiredOption("--output <path>", "Snapshot file to create or replace.")
-    .option("--label <label>", "Human-readable environment label.", "local")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (options, command) => {
-    const cwd = projectRoot(command);
-    const snapshot = await createTeamSnapshot({ cwd, label: options.label });
-    const outputPath = await writeTeamSnapshot(snapshot, path.resolve(cwd, options.output));
-    if (options.json) {
-        console.log(JSON.stringify({ outputPath, snapshot }, null, 2));
-        return;
-    }
-    console.log(pc.green("Team snapshot ready."));
-    console.log(`outputPath=${outputPath}`);
-    console.log(`label=${snapshot.label}`);
-    console.log(`ready=${snapshot.ready}`);
-    console.log(`securityAdvisories=${snapshot.health.securityWarnings}`);
-    console.log(`corpusFingerprint=${snapshot.corpus.fingerprint ?? "unavailable"}`);
-    console.log(`indexedFiles=${snapshot.corpus.indexedFiles}`);
-    console.log(`notice=${snapshot.notice}`);
-});
-teamCommand
-    .command("compare")
-    .description("Compare the current local index with a peer snapshot and print actionable drift.")
-    .argument("<snapshot>", "Peer snapshot created by `rgr team snapshot`.")
-    .option("--local-label <label>", "Human-readable label for this environment.", "local")
-    .option("--json", "Print machine-readable JSON.")
-    .option("--strict", "Exit with code 1 unless both indexes are synchronized.")
-    .action(async (snapshotPath, options, command) => {
-    const cwd = projectRoot(command);
-    const [local, peer] = await Promise.all([
-        createTeamSnapshot({ cwd, label: options.localLabel }),
-        readTeamSnapshot(path.resolve(cwd, snapshotPath)),
-    ]);
-    const comparison = compareTeamSnapshots(local, peer);
-    if (options.json) {
-        console.log(JSON.stringify(comparison, null, 2));
-    }
-    else {
-        printTeamComparison(comparison);
-    }
-    if (options.strict && !comparison.synchronized) {
-        process.exitCode = 1;
-    }
-});
 program
     .command("status")
     .description("Show active configuration, readiness, corpus fingerprint, and index counts.")
@@ -907,13 +680,10 @@ program
         rawDir: config.rawDir,
         storageDir: config.storageDir,
         sourcesFile: config.sourcesFile,
-        accessLogPath: config.accessLogPath,
         embeddingModelPath: config.embeddingModelPath,
         embeddingProvider: config.embeddingProvider,
         embeddingModel: config.embeddingModel,
         transformersAllowRemoteModels: config.transformersAllowRemoteModels,
-        redactionEnabled: config.redaction.enabled,
-        accessLog: config.accessLog,
         mcpMaxTopK: config.mcpMaxTopK,
         mcpMaxOutputBytes: config.mcpMaxOutputBytes,
         topK: config.topK,
@@ -949,13 +719,10 @@ program
     console.log(`rawDir=${config.rawDir}`);
     console.log(`storageDir=${config.storageDir}`);
     console.log(`sourcesFile=${config.sourcesFile}`);
-    console.log(`accessLogPath=${config.accessLogPath}`);
     console.log(`embeddingModelPath=${config.embeddingModelPath}`);
     console.log(`embeddingProvider=${config.embeddingProvider}`);
     console.log(`embeddingModel=${config.embeddingModel}`);
     console.log(`transformersAllowRemoteModels=${config.transformersAllowRemoteModels}`);
-    console.log(`redactionEnabled=${config.redaction.enabled}`);
-    console.log(`accessLog=${config.accessLog}`);
     console.log(`mcpMaxTopK=${config.mcpMaxTopK}`);
     console.log(`mcpMaxOutputBytes=${config.mcpMaxOutputBytes}`);
     console.log(`topK=${config.topK}`);
@@ -992,7 +759,7 @@ program
 });
 program
     .command("security-audit")
-    .description("Show local privacy, provider, redaction, MCP, and gitignore posture.")
+    .description("Show local providers, file permissions, MCP bounds, and Git exclusions.")
     .option("--json", "Print machine-readable JSON.")
     .option("--strict", "Exit with code 1 when warnings are present.")
     .action(async (options, command) => {
@@ -1008,10 +775,6 @@ program
         console.log(`embeddingModelPath=${report.providers.embeddingModelPath}`);
         console.log(`transformersAllowRemoteModels=${report.providers.transformersAllowRemoteModels}`);
         console.log(`llmGeneration=${report.providers.llmGeneration}`);
-        console.log(`redactionEnabled=${report.redaction.enabled}`);
-        console.log(`redactionBuiltIn=${report.redaction.builtIn}`);
-        console.log(`accessLog=${report.accessLog.enabled}`);
-        console.log(`accessLogStoresRawQueries=${report.accessLog.storesRawQueries}`);
         console.log(`storageGitIgnored=${report.storage.gitIgnored}`);
         console.log(`mcpMaxTopK=${report.mcp.maxTopK}`);
         console.log(`mcpMaxOutputBytes=${report.mcp.maxOutputBytes}`);
@@ -1100,131 +863,6 @@ program
     console.log(`removed=${result.removed}`);
     console.log(result.note);
 });
-program
-    .command("chat")
-    .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("--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("--json", "Print machine-readable JSON.")
-    .action(async (input, options, command) => {
-    const cwd = projectRoot(command);
-    const chat = await loadChat();
-    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, "profile", options.profile);
-        addOption(setupOptions, "modelPath", options.modelPath);
-        addOption(setupOptions, "allowRemoteModels", options.offline ? false : options.allowRemoteModels);
-        const result = await chat.setupChatModel(setupOptions);
-        printMaybeJson(result, options.json);
-        return;
-    }
-    const question = await promptInput(input);
-    if (question.trim().length === 0) {
-        console.error(pc.red('Missing question. Use `rgr chat "your question"`.'));
-        process.exitCode = 1;
-        return;
-    }
-    const sources = await search(question, withTopK(cwd, options.topK));
-    const chatOptions = {
-        cwd,
-        question,
-        sources: sources.map(toChatSource),
-    };
-    addOption(chatOptions, "profile", options.profile);
-    addOption(chatOptions, "thinking", options.thinking);
-    addOption(chatOptions, "modelPath", options.modelPath);
-    addOption(chatOptions, "allowRemoteModels", chatAllowRemoteModels(options));
-    addOption(chatOptions, "maxNewTokens", options.maxNewTokens);
-    addOption(chatOptions, "contextCharLimit", options.contextLimit);
-    const result = await chat.generateChatAnswer(chatOptions);
-    if (options.json) {
-        console.log(JSON.stringify({ query: question, ...result }, null, 2));
-        if (result.emptyContext) {
-            process.exitCode = 1;
-        }
-        return;
-    }
-    console.log(`\n${result.answer}\n`);
-    if (!result.emptyContext && result.citationStatus !== "valid") {
-        console.error(pc.yellow(`Citation status: ${result.citationStatus}. Review the answer against the retrieved passages.`));
-    }
-    if (result.sources.length > 0) {
-        console.log(pc.dim("Sources:"));
-        for (const [index, source] of result.sources.entries()) {
-            console.log(`  [${index + 1}] ${source.relativePath} chunk=${source.chunkIndex}`);
-        }
-    }
-    else {
-        const repairCommand = await rgrCommand(cwd, ["doctor", "--fix"]);
-        console.error(pc.yellow(`No Ragmir context found. Run \`${repairCommand.display}\`.`));
-        process.exitCode = 1;
-    }
-});
-program
-    .command("audio")
-    .description("Render narration as offline WAV or explicitly selected online Edge MP3.")
-    .argument("[text-file]", "Narration text file to render.")
-    .option("-o, --out <path>", "Output MP3 or WAV path.")
-    .option("--engine <engine>", "TTS engine: auto, edge, or transformers.")
-    .option("--lang <language>", "TTS language. Offline: en, es, fr. Edge also: ja, th, zh. Default: fr.")
-    .option("--model <id>", "Transformers.js TTS model ID.")
-    .option("--model-path <path>", "Local model/cache path.")
-    .option("--offline", "Force the Transformers.js local/offline WAV path.")
-    .option("--allow-remote-models", "Explicitly allow remote model downloads.")
-    .option("--voice <voice>", "Edge voice override. Default matches --lang.")
-    .option("--rate <rate>", "Edge rate. Defaults to +0%.")
-    .option("--speaker-embeddings <path>", "Optional model-specific speaker embedding path or URL.")
-    .option("--speed <number>", "Optional model-specific speech speed.", parseNumber)
-    .option("--doctor", "Show TTS runtime readiness instead of rendering.")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (textFile, options, command) => {
-    const cwd = projectRoot(command);
-    const tts = await loadTts();
-    if (options.doctor) {
-        const report = await tts.doctor();
-        printMaybeJson(report, options.json);
-        return;
-    }
-    if (!textFile) {
-        console.error(pc.red("Missing text file. Use `rgr audio <text-file>`."));
-        process.exitCode = 1;
-        return;
-    }
-    const renderOptions = {
-        cwd,
-        textFile,
-        engine: audioEngine(options),
-    };
-    addOption(renderOptions, "language", audioLanguage(options));
-    addOption(renderOptions, "outputPath", options.out);
-    addOption(renderOptions, "model", options.model);
-    addOption(renderOptions, "modelPath", options.modelPath);
-    addOption(renderOptions, "allowRemoteModels", audioAllowRemoteModels(options));
-    addOption(renderOptions, "voice", options.voice);
-    addOption(renderOptions, "rate", options.rate);
-    addOption(renderOptions, "speakerEmbeddings", options.speakerEmbeddings);
-    addOption(renderOptions, "speed", options.speed);
-    const result = await tts.renderSpeech(renderOptions);
-    printMaybeJson(result, options.json);
-});
 program
     .command("serve-mcp")
     .description("Start the MCP server over stdio for Claude, Codex, and other MCP-compatible agents.")
@@ -1232,65 +870,6 @@ program
     const explicitRoot = explicitProjectRoot(command);
     await serveMcp(explicitRoot);
 });
-const portableCommand = program
-    .command("portable")
-    .description("Export or verify a frozen, relocatable Ragmir knowledge-base folder.");
-portableCommand
-    .command("export")
-    .description("Export the active index, skills, launcher, and MCP adapters into one folder.")
-    .option("-o, --output <directory>", "Destination directory. Defaults under .ragmir/exports/.")
-    .option("--name <name>", "Portable knowledge-base display name.")
-    .option("--replace", "Replace an existing portable destination after preserving it as a sibling backup.")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (options, command) => {
-    const exportOptions = {
-        cwd: projectRoot(command),
-        replaceExisting: options.replace === true,
-    };
-    addOption(exportOptions, "outputDir", options.output);
-    addOption(exportOptions, "name", options.name);
-    const result = await exportPortableKnowledgeBase(exportOptions);
-    if (options.json) {
-        console.log(JSON.stringify(result, null, 2));
-        return;
-    }
-    console.log(pc.green("Portable knowledge base exported."));
-    console.log(`outputDir=${result.outputDir}`);
-    if (result.previousOutputDir) {
-        console.log(`previousOutputDir=${result.previousOutputDir}`);
-    }
-    console.log(`manifestPath=${result.manifestPath}`);
-    console.log(`fileCount=${result.fileCount}`);
-    console.log(`totalBytes=${result.totalBytes}`);
-    console.log(`embeddingModelIncluded=${result.embeddingModelIncluded}`);
-    console.log(result.previousOutputDir
-        ? "Next: verify the active destination, restart its consumers, then retire the preserved previous folder when safe."
-        : "Next: move the folder, then run `node bin/rgr.cjs portable verify . --json`.");
-});
-portableCommand
-    .command("verify")
-    .description("Verify file integrity, index compatibility, and active table readability.")
-    .argument("[directory]", "Portable knowledge-base directory.", ".")
-    .option("--json", "Print machine-readable JSON.")
-    .action(async (directory, options) => {
-    const result = await verifyPortableKnowledgeBase(directory);
-    if (options.json) {
-        console.log(JSON.stringify(result, null, 2));
-    }
-    else {
-        console.log(result.valid
-            ? pc.green("Portable knowledge base is valid.")
-            : pc.red("Portable knowledge base is invalid."));
-        console.log(`root=${result.root}`);
-        console.log(`checkedFiles=${result.checkedFiles}`);
-        for (const warning of result.warnings)
-            console.log(pc.yellow(`warning=${warning}`));
-        for (const error of result.errors)
-            console.log(pc.red(`error=${error}`));
-    }
-    if (!result.valid)
-        process.exitCode = 1;
-});
 program
     .command("skill-path")
     .description("Print the bundled Ragmir skill path for agents that can load SKILL.md folders.")
@@ -1324,8 +903,6 @@ program
         console.log(`  - ${file}`);
     }
     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: ${result.mcpConfigPath}`);
     for (const helper of result.agentHelpers) {
         console.log(`${helper.label} MCP helper: ${helper.path}`);
@@ -1395,25 +972,6 @@ function explicitProjectRoot(command) {
     const options = command.optsWithGlobals();
     return options.projectRoot ? path.resolve(options.projectRoot) : undefined;
 }
-function deprecatedCliInvocation() {
-    const invokedPath = process.argv[1];
-    if (!invokedPath)
-        return null;
-    const commandName = path.basename(invokedPath).replace(/\.(?:cmd|ps1)$/iu, "");
-    return DEPRECATED_CLI_NAMES.has(commandName) ? commandName : null;
-}
-async function promptInput(promptParts) {
-    if (promptParts !== undefined && promptParts.length > 0) {
-        return promptParts.join(" ");
-    }
-    if (process.stdin.isTTY) {
-        return "";
-    }
-    return readBoundedStdin(process.stdin);
-}
-function withTopK(cwd, topK) {
-    return topK === undefined ? { cwd } : { cwd, topK };
-}
 function withSearchOptions(cwd, options) {
     const result = { cwd };
     addOption(result, "topK", options.topK);
@@ -1437,89 +995,6 @@ function addPathFilters(target, options) {
         target.contextPaths = options.contextPath;
     }
 }
-async function loadChat() {
-    let module;
-    try {
-        module = await import(CHAT_PACKAGE_NAME);
-    }
-    catch (error) {
-        if (isMissingOptionalPackage(error, CHAT_PACKAGE_NAME)) {
-            throw new Error(`Ragmir Chat is optional and is not installed. Add ${CHAT_PACKAGE_NAME} to this project before using \`rgr chat\`.`);
-        }
-        throw error;
-    }
-    if (!isChatModule(module)) {
-        throw new Error(`${CHAT_PACKAGE_NAME} did not expose the expected chat API.`);
-    }
-    return module;
-}
-function isChatModule(value) {
-    return (typeof value === "object" &&
-        value !== null &&
-        "doctor" in value &&
-        typeof value.doctor === "function" &&
-        "generateChatAnswer" in value &&
-        typeof value.generateChatAnswer === "function" &&
-        "setupChatModel" in value &&
-        typeof value.setupChatModel === "function");
-}
-function chatMode(input) {
-    if (input?.length === 1 && input[0] === "doctor") {
-        return "doctor";
-    }
-    if (input?.length === 1 && input[0] === "setup") {
-        return "setup";
-    }
-    return "ask";
-}
-function chatAllowRemoteModels(options) {
-    if (options.offline) {
-        return false;
-    }
-    if (options.allowRemoteModels) {
-        return true;
-    }
-    return undefined;
-}
-function toChatSource(source) {
-    return {
-        source: source.source,
-        relativePath: source.relativePath,
-        chunkIndex: source.chunkIndex,
-        text: source.text,
-        distance: source.distance,
-    };
-}
-async function loadTts() {
-    let module;
-    try {
-        module = await import(TTS_PACKAGE_NAME);
-    }
-    catch (error) {
-        if (isMissingOptionalPackage(error, TTS_PACKAGE_NAME)) {
-            throw new Error(`Ragmir TTS is optional and is not installed. Add ${TTS_PACKAGE_NAME} to this project before using \`rgr audio\`.`);
-        }
-        throw error;
-    }
-    if (!isTtsModule(module)) {
-        throw new Error(`${TTS_PACKAGE_NAME} did not expose the expected TTS API.`);
-    }
-    return module;
-}
-function isMissingOptionalPackage(error, packageName) {
-    return (error instanceof Error &&
-        "code" in error &&
-        error.code === "ERR_MODULE_NOT_FOUND" &&
-        error.message.includes(packageName));
-}
-function isTtsModule(value) {
-    return (typeof value === "object" &&
-        value !== null &&
-        "doctor" in value &&
-        typeof value.doctor === "function" &&
-        "renderSpeech" in value &&
-        typeof value.renderSpeech === "function");
-}
 function printDoctor(report) {
     console.log(`mode=${report.mode}`);
     console.log(`cost=${report.cost}`);
@@ -1551,8 +1026,6 @@ function printDoctor(report) {
     }
     console.log(`embeddingProvider=${report.embeddingProvider}`);
     console.log(`transformersAllowRemoteModels=${report.transformersAllowRemoteModels}`);
-    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}`);
@@ -1633,148 +1106,7 @@ function printGenerationGarbageCollection(report) {
         console.log(pc.yellow(`warning: ${report.warning}`));
     }
 }
-function printResearchReport(report) {
-    console.log(`query=${report.query}`);
-    console.log(`ready=${report.ready}`);
-    console.log(`generatedQueries=${report.generatedQueries.length}`);
-    console.log(`audit.mode=${report.audit.mode} audit.inventoryVerified=${report.audit.inventoryVerified} 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=${report.audit.staleInIndex}`);
-    console.log(`budgets.timeoutMs=${report.budgets.timeoutMs ?? "none"} budgets.evidenceTopK=${report.budgets.evidenceTopK} budgets.codeEvidenceTopK=${report.budgets.codeEvidenceTopK} budgets.codeFiles=${report.budgets.codeFilesScanned}/${report.budgets.codeScanMaxFiles} budgets.codeBytes=${report.budgets.codeBytesScanned}/${report.budgets.codeScanMaxBytes} budgets.codeConcurrency=${report.budgets.codeScanConcurrency} budgets.codeTruncated=${report.budgets.codeScanTruncated}`);
-    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) {
-        console.log("");
-        console.log(pc.cyan("Duplicate Candidates:"));
-        for (const candidate of report.sourceDiagnostics.duplicateCandidates.slice(0, 5)) {
-            console.log(`  - ${candidate.key}: ${candidate.files.join(", ")}`);
-        }
-    }
-    if (report.evidence.length > 0) {
-        console.log("");
-        console.log(pc.cyan("Evidence:"));
-        for (const [index, evidence] of report.evidence.entries()) {
-            const distance = evidence.distance === null ? "n/a" : evidence.distance.toFixed(4);
-            console.log(`  [${index + 1}] ${evidence.relativePath} chunk=${evidence.chunkIndex} distance=${distance} researchScore=${evidence.researchScore.toFixed(6)} bestRank=${evidence.bestRank}`);
-            console.log(`      ${researchEvidencePreview(evidence)}`);
-        }
-    }
-    if (report.codeEvidence.length > 0) {
-        console.log("");
-        console.log(pc.cyan("Code Evidence:"));
-        for (const evidence of report.codeEvidence.slice(0, 10)) {
-            console.log(`  - ${evidence.relativePath}:${evidence.lineNumber} score=${evidence.score} terms=${evidence.matchedTerms.join(",")}`);
-            console.log(`      ${evidence.snippet}`);
-        }
-    }
-    if (report.gaps.length > 0) {
-        console.log("");
-        console.log(pc.yellow("Gaps:"));
-        for (const gap of report.gaps) {
-            console.log(pc.yellow(`  - ${gap}`));
-        }
-    }
-    console.log("");
-    console.log(pc.cyan("Next Steps:"));
-    for (const step of report.nextSteps) {
-        console.log(`  - ${step}`);
-    }
-}
-function researchEvidencePreview(evidence) {
-    if ("snippet" in evidence) {
-        return evidence.snippet;
-    }
-    return evidence.text.replace(/\s+/gu, " ").trim().slice(0, SEARCH_TEXT_PREVIEW_LENGTH);
-}
-function printTeamComparison(comparison) {
-    const statusColor = comparison.synchronized ? pc.green : pc.yellow;
-    console.log(statusColor(`Team status: ${comparison.status}`));
-    console.log(`summary=${comparison.summary}`);
-    console.log(`local=${comparison.localLabel}`);
-    console.log(`peer=${comparison.peerLabel}`);
-    console.log(`localSecurityAdvisories=${comparison.securityAdvisories.local}`);
-    console.log(`peerSecurityAdvisories=${comparison.securityAdvisories.peer}`);
-    console.log(`sameConfiguration=${comparison.sameConfiguration}`);
-    console.log(`sameCorpus=${comparison.sameCorpus}`);
-    console.log(`authorityDecisionRequired=${comparison.authorityDecisionRequired}`);
-    if (comparison.configurationDifferences.length > 0) {
-        console.log("");
-        console.log(pc.cyan("Configuration differences:"));
-        for (const difference of comparison.configurationDifferences) {
-            console.log(`  - ${difference.field} (${difference.scope}, rebuild=${difference.requiresRebuild}): local=${formatTeamValue(difference.local)} peer=${formatTeamValue(difference.peer)}`);
-        }
-    }
-    printTeamPaths("Local-only files", comparison.files.localOnly);
-    printTeamPaths("Peer-only files", comparison.files.peerOnly);
-    if (comparison.files.changed.length > 0) {
-        console.log("");
-        console.log(pc.cyan(`Changed files (${comparison.files.changed.length}):`));
-        for (const file of comparison.files.changed.slice(0, TEAM_DIFF_PREVIEW_LIMIT)) {
-            console.log(`  - ${file.relativePath} local=${file.localChecksum.slice(0, 12)} peer=${file.peerChecksum.slice(0, 12)}`);
-        }
-        printTeamOmitted(comparison.files.changed.length);
-    }
-    if (comparison.recommendedActions.length > 0) {
-        console.log("");
-        console.log(pc.cyan("Recommended actions:"));
-        for (const [index, action] of comparison.recommendedActions.entries()) {
-            console.log(`  ${index + 1}. ${action}`);
-        }
-    }
-}
-function printTeamSync(report) {
-    const statusColor = report.synchronized
-        ? pc.green
-        : report.status === "index-not-ready"
-            ? pc.red
-            : pc.yellow;
-    console.log(statusColor(`Team sync: ${report.status}`));
-    console.log(`summary=${report.summary}`);
-    console.log(`gitState=${report.git.state}`);
-    console.log(`branch=${report.git.branch ?? "none"}`);
-    console.log(`upstream=${report.git.upstream ?? "none"}`);
-    console.log(`ahead=${report.git.ahead ?? "unknown"}`);
-    console.log(`behind=${report.git.behind ?? "unknown"}`);
-    console.log(`dirty=${report.git.dirty ?? "unknown"}`);
-    console.log(`fetched=${report.git.fetched}`);
-    console.log(`updated=${report.git.updated}`);
-    console.log(`indexReady=${report.index.operationalReady && report.index.indexPolicyCurrent}`);
-    console.log(`indexedFiles=${report.index.indexedFiles}`);
-    console.log(`chunksIndexed=${report.index.chunksIndexed}`);
-    console.log(`securityAdvisories=${report.index.securityAdvisories}`);
-    if (report.warnings.length > 0) {
-        console.log("");
-        console.log(pc.yellow("Warnings:"));
-        for (const warning of report.warnings) {
-            console.log(`  - ${warning}`);
-        }
-    }
-    if (report.recommendedActions.length > 0) {
-        console.log("");
-        console.log(pc.cyan("Next action:"));
-        console.log(`  ${report.recommendedActions[0]}`);
-    }
-}
-function printTeamPaths(title, files) {
-    if (files.length === 0) {
-        return;
-    }
-    console.log("");
-    console.log(pc.cyan(`${title} (${files.length}):`));
-    for (const file of files.slice(0, TEAM_DIFF_PREVIEW_LIMIT)) {
-        console.log(`  - ${file}`);
-    }
-    printTeamOmitted(files.length);
-}
-function printTeamOmitted(total) {
-    const omitted = total - TEAM_DIFF_PREVIEW_LIMIT;
-    if (omitted > 0) {
-        console.log(`  ... ${omitted} more; use --json for the complete diff.`);
-    }
-}
-function formatTeamValue(value) {
-    return Array.isArray(value) ? JSON.stringify(value) : String(value);
-}
 function printPdfOcrStatus(status) {
-    console.log(`privacyProfile=${status.privacyProfile}`);
     console.log(`configured=${status.configured}`);
     console.log(`recommendedEngine=${status.recommendedEngine ?? "none"}`);
     console.log(`ocrmypdf.available=${status.ocrmypdf.available}`);
@@ -1785,15 +1117,6 @@ function printPdfOcrStatus(status) {
     console.log(`pdftoppm.available=${status.pdftoppm.available}`);
     console.log(`pdftoppm.version=${status.pdftoppm.version ?? "unavailable"}`);
     console.log(`languages=${status.languages.join(",")}`);
-    if (status.privacyProfile === "strict") {
-        console.log(pc.yellow("The strict privacy profile disables external OCR even when local tools are installed."));
-    }
-    else if (!status.recommendedEngine) {
-        console.log(pc.yellow("Install OCRmyPDF 12.6+ or install both Tesseract and Poppler, then run `rgr ocr setup`."));
-    }
-    else if (!status.configured) {
-        console.log(`Run \`rgr ocr setup --engine ${status.recommendedEngine}\` to enable local PDF OCR.`);
-    }
 }
 function printSetup(result, title) {
     console.log(pc.green(title));
@@ -1813,8 +1136,6 @@ function printSetup(result, title) {
     console.log("");
     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}`);
     for (const helper of result.agentKit.agentHelpers) {
         console.log(`  - ${helper.label} MCP helper: ${helper.path}`);
@@ -1878,19 +1199,6 @@ function printEmptyTextFiles(files) {
     }
     console.log(pc.yellow("These supported files produced no indexable text. For scanned PDFs, run `rgr ocr doctor` then `rgr ocr setup`; for images, configure imageOcrCommand or store local OCR text beside the source file."));
 }
-function printMaybeJson(value, json) {
-    if (json) {
-        console.log(JSON.stringify(value, null, 2));
-        return;
-    }
-    if (typeof value === "object" && value !== null) {
-        for (const [key, entry] of Object.entries(value)) {
-            console.log(`${key}=${String(entry)}`);
-        }
-        return;
-    }
-    console.log(String(value));
-}
 function addOption(target, key, value) {
     if (value !== undefined) {
         target[key] = value;