@djolex999/vir-cli 0.23.3 → 0.24.2

package/dist/cli.js

@@ -1,26 +1,18 @@
 #!/usr/bin/env node
-import confirm from "@inquirer/confirm";
-import input from "@inquirer/input";
-import select from "@inquirer/select";
 import chalk from "chalk";
 import { Command } from "commander";
 import { createInterface } from "node:readline/promises";
 import { stdin, stdout, argv } from "node:process";
-import { existsSync, mkdirSync, readFileSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { basename, dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";
-import { CONFIG_PATH, maskSecret, ConfigSchema, configExists, ensureVirDir, expandHome, loadConfig, saveConfig, } from "./config.js";
+import { configExists, loadConfig } from "./config.js";
 import { applyPlan, planUpdates } from "./claude/updater.js";
 import { pruneCommand } from "./cli/pruneAction.js";
 import { setupNotifications } from "./cli/notificationsSetup.js";
-import { detectDuplicates } from "./dedupe/detector.js";
-import { mergeNotes } from "./dedupe/merger.js";
-import { contradictionCheck, orphanCheck, stalenessCheck, } from "./lint/linter.js";
-import { legacyRelatedCheck, migrateLegacyRelated, } from "./lint/legacyRelated.js";
-import { demoteStrays, strayFileCheck } from "./lint/strayFiles.js";
 import { runPipeline } from "./pipeline/run.js";
-import { categorizeTranscriptHead, classifyTranscript, estimateSessionCost, groupByProject, projectNameFor, readTranscriptHead, } from "./pipeline/projects.js";
+import { projectNameFor } from "./pipeline/projects.js";
 import { persistProjectDecisions, promptProjectDecisions, } from "./cli/projectSelect.js";
 import { gatherProjectsReport } from "./cli/projects.js";
 import { scanSessions } from "./pipeline/scanner.js";
@@ -28,15 +20,7 @@ import { parseSession } from "./pipeline/parser.js";
 import { scoreSession } from "./pipeline/filter.js";
 import { scrub } from "./pipeline/scrubber.js";
 import { filterToolCalls } from "./pipeline/toolCallFilter.js";
-import { Distiller, callLLM, maybeAnthropicClient, normalizeModelName, resolveModelShorthand, withRateLimitRetry, } from "./pipeline/distiller.js";
-import { applyAuditRejects, previewRejects } from "./audit/apply.js";
-import { batchByProject } from "./audit/batch.js";
-import { noteIsVerified, parseLimitOption, runAudit, selectAuditRows } from "./audit/run.js";
-import { composeFromSources, estimateComposeCostTokens, gatherSources, } from "./pipeline/composer.js";
-import { computeCost } from "./cost/pricing.js";
-import { countByCategory, summarizeAll, summarizeProject, } from "./pipeline/summarizer.js";
-import { buildPeriodPrompt, estimatePeriodCostTokens, periodLabel, periodRange, selectNotesInPeriod, summarizePeriod, } from "./pipeline/periodSummary.js";
-import { embedNoteWithProvider, resolveEmbeddingProvider, } from "./search/provider.js";
+import { Distiller } from "./pipeline/distiller.js";
 import { acquireLock, LockHeldError, releaseLock } from "./pipeline/lock.js";
 import { loadIndex, searchWithOutcome, vaultRoot } from "./search/retriever.js";
 import { QUERY_LOG_PATH, readQueryLog, recordQueryEvent, } from "./search/queryLog.js";
@@ -47,9 +31,7 @@ import { runMcpServer } from "./mcp/server.js";
 import { runReview } from "./cli/review.js";
 import { runReviewJson } from "./cli/reviewJson.js";
 import { runAction } from "./cli/runAction.js";
-import { buildInitConfig } from "./cli/initConfig.js";
 import { runReconcile } from "./cli/reconcile.js";
-import { runEmbedSetup } from "./cli/embedSetup.js";
 import { installToClaudeCode, isClaudeAvailable, isInstalled, uninstallFromClaudeCode, } from "./mcp/install.js";
 import { install as installDaemon, status as daemonStatus, uninstall as uninstallDaemon, } from "./daemon/index.js";
 import { StateDb } from "./state/db.js";
@@ -57,7 +39,15 @@ import { parseDuration, readCostLog } from "./cost/log.js";
 import { buildReport } from "./cost/report.js";
 import * as ui from "./ui/display.js";
 import { VaultWriter } from "./pipeline/writer.js";
+import { withPipelineLock } from "./cli/guards.js";
 import { runDoctor, runDoctorJson } from "./diagnostics/doctor.js";
+import { embedCommand } from "./cli/embed.js";
+import { lintCommand } from "./cli/lint.js";
+import { summarizeCommand } from "./cli/summarize.js";
+import { auditCommand } from "./cli/audit.js";
+import { composeCommand } from "./cli/compose.js";
+import { dedupeCommand } from "./cli/dedupe.js";
+import { cmdInit } from "./cli/init.js";
 // Read version at runtime from package.json (one dir up from dist/cli.js) so
 // `vir --version` never drifts from the published version. rootDir is ./src,
 // so package.json can't be imported — read it instead.
@@ -149,7 +139,7 @@ program
                 : undefined,
             onConfirm: skipPrompt
                 ? undefined
-                : async (newCount) => confirmCostIfNeeded(cfg, newCount),
+                : async (newCount, estimatedUsd) => confirmCostIfNeeded(cfg, newCount, estimatedUsd),
         });
     }
     finally {
@@ -168,21 +158,18 @@ program
         process.exitCode = 1;
     }
 }));
-// Dollar-estimate label for the ACTIVE provider. On the subscription path the
-// honest label is quota, never "$0.00" — a zero would read as "free API call"
-// and hide that the run consumes the user's Claude Code limits.
-function estCostLabel(cfg, model, inputTokens, outputTokens) {
-    if (cfg.provider === "claude-cli")
-        return "subscription quota (no $)";
-    return ui.formatUsd(computeCost(cfg.provider, model, inputTokens, outputTokens, cfg.pricing, cfg.kieTopUpTier));
-}
-async function confirmCostIfNeeded(cfg, newCount) {
+async function confirmCostIfNeeded(cfg, newCount, estimatedUsd) {
     if (newCount <= 20)
         return true;
+    // Upper bound from transcript sizes; sessions the filter drops cost nothing.
+    const estimate = cfg.provider === "claude-cli"
+        ? "subscription quota (no $)"
+        : estimatedUsd === null
+            ? "unknown (no price for the configured models)"
+            : `up to ${ui.formatUsd(estimatedUsd)}`;
     ui.box([
         `${ui.text(String(newCount))} ${ui.dim("new sessions to process")}`,
-        `${ui.dim("estimated:")} ${ui.warn("$1–5")} ${ui.dim("depending on session")}`,
-        `${ui.dim("depth (deep code reviews cost more)")}`,
+        `${ui.dim("estimated:")} ${ui.warn(estimate)} ${ui.dim("(filtered sessions cost nothing)")}`,
         `${ui.dim("provider:")} ${ui.accent(cfg.provider)}`,
     ], { title: "cost estimate" });
     const rl = createInterface({ input: stdin, output: stdout });
@@ -223,6 +210,9 @@ program
     if (report.subscriptionCalls > 0) {
         ui.stat("subscription", `${report.subscriptionCalls} claude-cli calls (quota, no $ — excluded from totals)`);
     }
+    if (report.unpricedCalls > 0) {
+        ui.stat("unpriced", `${report.unpricedCalls} calls to a model with no price (real spend, not in the total — add it under pricing in config.json)`, ui.warn);
+    }
     ui.stat("sessions", report.sessionCount);
     ui.stat("total", ui.formatUsd(report.total), ui.warn);
     ui.stat("median/session", ui.formatUsd(report.median));
@@ -408,6 +398,9 @@ program
                 continue;
             }
             const result = applyPlan(p);
+            // A file that could not be updated is a failed sync, not a warning.
+            if (!result.ok)
+                process.exitCode = 1;
             ui.row(result.ok ? ui.success(ui.CHECK) : ui.errorColor(ui.CROSS), ui.text(result.ok || result.reason === undefined
                 ? collapseHome(p.target)
                 : `${collapseHome(p.target)} — ${result.reason}`));
@@ -420,73 +413,8 @@ program
 program
     .command("dedupe")
     .description("Interactive duplicate detection + merge")
-    .action(runAction(async () => {
-    const cfg = loadConfig();
-    const db = new StateDb();
-    try {
-        console.log("scanning for duplicate candidates...");
-        const result = await detectDuplicates(cfg, db);
-        console.log(`${result.checked} candidate pairs checked, ${result.duplicates.length} flagged as duplicates`);
-        if (result.duplicates.length === 0) {
-            return;
-        }
-        const rl = createInterface({ input: stdin, output: stdout });
-        let merged = 0;
-        let skipped = 0;
-        for (const dup of result.duplicates) {
-            console.log("\nDuplicate found:");
-            console.log(`A: ${noteRefOf(dup.a)} (conf: ${dup.a.confidence.toFixed(2)}, ${dup.a.startedAt?.slice(0, 10) ?? "?"})`);
-            console.log(`   "${preview(dup.a.content)}"`);
-            console.log(`B: ${noteRefOf(dup.b)} (conf: ${dup.b.confidence.toFixed(2)}, ${dup.b.startedAt?.slice(0, 10) ?? "?"})`);
-            console.log(`   "${preview(dup.b.content)}"`);
-            console.log(`Reason: ${dup.reason}`);
-            const suggestion = dup.keepWhich === "merge"
-                ? "merge both"
-                : `keep ${dup.keepWhich}`;
-            console.log(`Suggested: ${suggestion}`);
-            const ans = (await rl.question("[k]eep suggestion / [s]wap / [m]erge / [x] skip: "))
-                .trim()
-                .toLowerCase();
-            let action = null;
-            if (ans === "k" || ans === "") {
-                action = dup.keepWhich;
-            }
-            else if (ans === "s") {
-                action =
-                    dup.keepWhich === "A"
-                        ? "B"
-                        : dup.keepWhich === "B"
-                            ? "A"
-                            : "merge";
-            }
-            else if (ans === "m") {
-                action = "merge";
-            }
-            else if (ans === "x") {
-                skipped += 1;
-                continue;
-            }
-            else {
-                console.log(chalk.yellow("unknown input — skipping"));
-                skipped += 1;
-                continue;
-            }
-            try {
-                const outcome = await mergeNotes(cfg, db, dup.a, dup.b, action);
-                merged += 1;
-                console.log(chalk.green(`merged (${outcome.action}): winner=${outcome.winnerPath} archived=${outcome.archivedPath}`));
-            }
-            catch (err) {
-                console.error(chalk.red(`merge failed: ${err.message}`));
-            }
-        }
-        rl.close();
-        console.log(`\n${result.duplicates.length} pairs reviewed, ${merged} merged, ${skipped} skipped.`);
-    }
-    finally {
-        db.close();
-    }
-}));
+    .option("--yes", "Skip the cost confirmation prompt")
+    .action(runAction(dedupeCommand));
 program
     .command("lint")
     .description("Run orphan, stray-file, legacy-Related, staleness, and contradiction checks on the vault")
@@ -496,156 +424,8 @@ program
     .option("--fix", "Move retitle-duplicate strays into archived/ (other strays are left alone), and move legacy Related content into ## Details")
     .option("--stale", "Run only the staleness check (free)")
     .option("--contradictions", "Run only the contradiction check (Haiku tokens)")
-    .action(runAction(async (opts) => {
-    const cfg = loadConfig();
-    const db = new StateDb();
-    try {
-        const runAll = !opts.orphans &&
-            !opts.strays &&
-            !opts.legacyRelated &&
-            !opts.stale &&
-            !opts.contradictions;
-        const checks = [];
-        if (runAll || opts.orphans)
-            checks.push("orphans");
-        if (runAll || opts.strays)
-            checks.push("strays");
-        if (runAll || opts.legacyRelated)
-            checks.push("legacy-related");
-        if (runAll || opts.stale)
-            checks.push("stale");
-        if (runAll || opts.contradictions)
-            checks.push("contradictions");
-        ui.header("lint");
-        ui.blank();
-        let orphanCount = 0;
-        let strayCount = 0;
-        let legacyCount = 0;
-        let staleCount = 0;
-        let contradictionCount = 0;
-        let issues = 0;
-        if (runAll || opts.orphans) {
-            const sp = ui.spinner("checking orphans").start();
-            const r = orphanCheck(cfg);
-            sp.stop();
-            orphanCount = r.orphans.length;
-            issues += orphanCount;
-            if (orphanCount === 0) {
-                ui.row(ui.success(ui.CHECK), `${ui.text("orphans")}  ${ui.dim("none")}`);
-            }
-            else {
-                ui.row(ui.errorColor(ui.CROSS), `${ui.text("orphans")} ${ui.dim("(" + orphanCount + ")")}`);
-                for (const o of r.orphans) {
-                    console.log(`   ${ui.dim(ui.BULLET)} ${ui.text(ui.shortNotePath(o))}`);
-                }
-            }
-        }
-        if (runAll || opts.strays) {
-            const sp = ui.spinner("checking stray files").start();
-            const r = strayFileCheck(cfg, db);
-            sp.stop();
-            strayCount = r.strays.length;
-            issues += strayCount;
-            if (strayCount === 0) {
-                ui.row(ui.success(ui.CHECK), `${ui.text("strays")}   ${ui.dim("none")}`);
-            }
-            else {
-                ui.row(ui.errorColor(ui.CROSS), `${ui.text("strays")} ${ui.dim("(" + strayCount + " of " + r.scanned + " files)")}`);
-                for (const st of r.strays) {
-                    // The sibling is the whole point: it is what makes a stray safe
-                    // to demote. An `unknown` stray has none, and gets no advice.
-                    const note = st.liveSibling !== null
-                        ? ui.dim(`${ui.ARROW} live: ${st.liveSibling}`)
-                        : ui.warn("only copy — inspect before removing");
-                    console.log(`   ${ui.dim(ui.BULLET)} ${ui.text(ui.shortNotePath(st.relPath))}  ${ui.muted(st.kind)}  ${note}`);
-                }
-                if (opts.fix) {
-                    const fixed = demoteStrays(cfg, r);
-                    strayCount -= fixed.moved;
-                    issues -= fixed.moved;
-                    ui.row(ui.success(ui.CHECK), `${ui.text("strays")} ${ui.dim(`moved ${fixed.moved} to archived/, left ${fixed.left} untouched`)}`);
-                }
-            }
-        }
-        if (runAll || opts.legacyRelated) {
-            const sp = ui.spinner("checking legacy Related sections").start();
-            const r = legacyRelatedCheck(db);
-            sp.stop();
-            const withContent = r.rows.filter((x) => x.kept > 0);
-            legacyCount = r.rows.length;
-            issues += legacyCount;
-            if (legacyCount === 0) {
-                ui.row(ui.success(ui.CHECK), `${ui.text("legacy-related")}  ${ui.dim("none")}`);
-            }
-            else {
-                const bullets = withContent.reduce((n, x) => n + x.kept, 0);
-                ui.row(ui.errorColor(ui.CROSS), `${ui.text("legacy-related")} ${ui.dim(`(${legacyCount} of ${r.scanned} stored notes; ${withContent.length} hold ${bullets} content bullets a rewrite drops)`)}`);
-                if (opts.fix) {
-                    const fixed = await migrateLegacyRelated(db, new VaultWriter(cfg, db));
-                    legacyCount -= fixed.migrated;
-                    issues -= fixed.migrated;
-                    ui.row(ui.success(ui.CHECK), `${ui.text("legacy-related")} ${ui.dim(`moved content into ## Details on ${fixed.migrated} rows, re-rendered ${fixed.rewritten} notes`)}`);
-                    for (const e of fixed.errors) {
-                        console.log(`   ${ui.dim(ui.BULLET)} ${ui.errorColor(e.path)}  ${ui.muted(e.message)}`);
-                    }
-                }
-                else {
-                    console.log(`   ${ui.dim(ui.ARROW)} ${ui.muted("vir lint --legacy-related --fix")}`);
-                }
-            }
-        }
-        if (runAll || opts.stale) {
-            const sp = ui.spinner("checking staleness").start();
-            const stale = stalenessCheck(cfg, db);
-            sp.stop();
-            staleCount = stale.length;
-            issues += staleCount;
-            if (staleCount === 0) {
-                ui.row(ui.success(ui.CHECK), `${ui.text("stale")}    ${ui.dim("none")}`);
-            }
-            else {
-                ui.row(ui.errorColor(ui.CROSS), `${ui.text("stale")} ${ui.dim("(" + staleCount + ")")}`);
-                for (const s of stale) {
-                    console.log(`   ${ui.dim(ui.BULLET)} ${ui.text(ui.shortNotePath(s.relPath))}  ${ui.muted(`${s.ageDays}d`)}  ${ui.dim(`${s.newerSameProjectCount} newer ${s.project} sessions`)}`);
-                }
-            }
-        }
-        if (runAll || opts.contradictions) {
-            const sp = ui.spinner("checking contradictions (haiku)").start();
-            const c = await contradictionCheck(cfg, db);
-            sp.stop();
-            contradictionCount = c.contradictions.length;
-            issues += contradictionCount;
-            if (contradictionCount === 0) {
-                ui.row(ui.success(ui.CHECK), `${ui.text("contradictions")}  ${ui.dim(`none found in ${c.checked} pairs`)}`);
-            }
-            else {
-                ui.row(ui.errorColor(ui.CROSS), `${ui.text("contradictions")} ${ui.dim("(" + contradictionCount + ")")}`);
-                for (const x of c.contradictions) {
-                    console.log(`   ${ui.dim(ui.BULLET)} ${ui.text(ui.shortNotePath(x.a))} ${ui.dim("vs")} ${ui.text(ui.shortNotePath(x.b))}`);
-                    console.log(`     ${ui.muted(x.reason)}`);
-                }
-            }
-        }
-        ui.blank();
-        ui.divider();
-        ui.summary({
-            issues: {
-                value: issues,
-                color: issues > 0 ? ui.errorColor : ui.success,
-            },
-            orphans: { value: orphanCount, color: ui.muted },
-            strays: { value: strayCount, color: ui.muted },
-            "legacy-related": { value: legacyCount, color: ui.muted },
-            stale: { value: staleCount, color: ui.muted },
-            contradictions: { value: contradictionCount, color: ui.muted },
-        });
-        ui.divider();
-    }
-    finally {
-        db.close();
-    }
-}));
+    .option("--yes", "Skip the cost confirmation for the contradiction check")
+    .action(runAction(lintCommand));
 program
     .command("summarize [project]")
     .description("Generate a project, --all, or period (--week/--month) knowledge summary")
@@ -655,304 +435,14 @@ program
     .option("--model <model>", "Synthesis model: haiku | sonnet (period only)")
     .option("--dry-run", "Show note count + estimated cost, exit before LLM")
     .option("--yes", "Skip the cost confirmation prompt (period only)")
-    .action(runAction(async (project, opts) => {
-    const cfg = loadConfig();
-    const wantWeek = opts.week !== undefined;
-    const wantMonth = opts.month !== undefined;
-    if (wantWeek && wantMonth) {
-        console.error(chalk.red("use --week or --month, not both"));
-        process.exitCode = 1;
-        return;
-    }
-    // ── period summary path (--week / --month) ──────────────────────────
-    if (wantWeek || wantMonth) {
-        if (project || opts.all) {
-            console.error(chalk.red("--week/--month cannot be combined with a project or --all"));
-            process.exitCode = 1;
-            return;
-        }
-        if (opts.model && !["haiku", "sonnet"].includes(opts.model)) {
-            console.error(chalk.red(`--model must be 'haiku' or 'sonnet', got '${opts.model}'`));
-            process.exitCode = 1;
-            return;
-        }
-        const kind = wantWeek ? "week" : "month";
-        const raw = wantWeek ? opts.week : opts.month;
-        // commander yields `true` for a bare flag, or the string value for `--week 2`
-        const offset = typeof raw === "string" ? Number.parseInt(raw, 10) : 0;
-        if (!Number.isInteger(offset) || offset < 0) {
-            console.error(chalk.red(`--${kind} offset must be a non-negative integer`));
-            process.exitCode = 1;
-            return;
-        }
-        const period = { kind, offset };
-        const now = new Date();
-        const db = new StateDb();
-        try {
-            ui.header("summarize");
-            ui.divider();
-            const range = periodRange(period, now);
-            const label = periodLabel(period, range);
-            console.log(ui.text(label));
-            ui.divider();
-            ui.blank();
-            const notes = selectNotesInPeriod(db.listDistilled(), period, now);
-            if (notes.length === 0) {
-                ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`no notes distilled in ${label} — nothing to summarize`));
-                ui.line(ui.dim("  run `vir run` to distill more sessions first"));
-                return;
-            }
-            const model = normalizeModelName(resolveModelShorthand(opts.model ?? cfg.models.distill), cfg.provider);
-            const counts = countByCategory(notes);
-            const prompt = buildPeriodPrompt(label, notes, counts);
-            const { inputTokens, outputTokens } = estimatePeriodCostTokens(prompt);
-            const estCost = estCostLabel(cfg, model, inputTokens, outputTokens);
-            ui.summary({
-                notes: { value: notes.length, color: ui.info },
-                model: { value: model, color: ui.accent },
-                "est. cost": { value: estCost, color: ui.warn },
-            });
-            ui.divider();
-            if (opts.dryRun === true) {
-                ui.line(ui.dim("  dry run — no synthesis performed; actuals may vary ±30%"));
-                return;
-            }
-            if (opts.yes !== true) {
-                const proceed = await confirm({
-                    message: `synthesize with ${model} (~${estCost})?`,
-                    default: true,
-                });
-                if (!proceed) {
-                    ui.line(ui.dim("aborted"));
-                    return;
-                }
-            }
-            const sp = ui.spinner("synthesizing period summary").start();
-            let result;
-            try {
-                result = await summarizePeriod(cfg, db, period, {
-                    now,
-                    model: opts.model,
-                });
-                sp.stop();
-            }
-            catch (err) {
-                sp.fail(ui.errorColor(err.message));
-                process.exitCode = 1;
-                return;
-            }
-            if (!result) {
-                ui.row(ui.warn(ui.WARN_GLYPH), ui.text("nothing to summarize"));
-                return;
-            }
-            ui.row(ui.success(ui.CHECK), ui.text(`wrote ${result.relPath} (${result.noteCount} notes)`));
-            ui.blank();
-        }
-        finally {
-            db.close();
-        }
-        return;
-    }
-    // ── project / --all path (unchanged) ────────────────────────────────
-    const db = new StateDb();
-    try {
-        if (opts.all) {
-            const results = await summarizeAll(cfg, db);
-            if (results.length === 0) {
-                console.log(chalk.yellow("no projects with notes"));
-                return;
-            }
-            for (const r of results) {
-                console.log(chalk.green(`summarized project/${r.slug}`) +
-                    ` (${r.counts.total} sessions)`);
-            }
-            return;
-        }
-        if (!project) {
-            console.error(chalk.red("usage: vir summarize <project> | --all | --week [n] | --month [n]"));
-            process.exitCode = 1;
-            return;
-        }
-        const res = await summarizeProject(cfg, project, db);
-        if (!res) {
-            console.log(chalk.yellow(`no distilled notes for project '${project}'`));
-            return;
-        }
-        console.log(chalk.green(`summarized project/${res.slug}`) +
-            ` (${res.counts.total} sessions) → ${res.path}`);
-    }
-    finally {
-        db.close();
-    }
-}));
+    .action(runAction(summarizeCommand));
 program
     .command("embed")
     .description("Generate embeddings for distilled notes")
     .option("--force", "Regenerate even if embedding already exists")
     .option("--setup", "Install the local embedding provider (fastembed + bge-small) on demand")
     .option("--yes", "Skip the --setup disk-cost confirmation")
-    .action(runAction(async (opts) => {
-    if (opts.setup) {
-        await runEmbedSetup(opts.yes === true);
-        return;
-    }
-    const cfg = loadConfig();
-    ui.header("embed");
-    ui.blank();
-    const provider = await resolveEmbeddingProvider(cfg.embeddingProvider);
-    if (!provider) {
-        ui.row(ui.errorColor(ui.CROSS), ui.text("no embedding provider available"));
-        ui.line(ui.dim("  vir embed --setup      # local provider, no Ollama needed (~233 MB)"));
-        ui.line(ui.dim("  or: brew install ollama && ollama pull nomic-embed-text && ollama serve"));
-        process.exitCode = 1;
-        return;
-    }
-    const provenance = provider.provenance();
-    const db = new StateDb();
-    try {
-        const rows = db.listDistilled();
-        const root = join(cfg.vaultPath, cfg.outputDir);
-        const embeddedRows = [
-            ...db.getEmbeddings(root),
-            ...db.getArticleEmbeddings(),
-            ...db.getTopicEmbeddings(root, cfg.topicsDir),
-            ...db.getPdfEmbeddings(),
-        ];
-        // Crossing a model boundary is an index invalidation, not a gap fill —
-        // it needs --force AND explicit consent, with the cost stated first.
-        // Without --force, mismatched rows stay excluded from vector search
-        // (counted, reported) and only NULL-embedding gaps are filled.
-        const mismatched = embeddedRows.filter((r) => r.embeddingModel !== provider.modelName).length;
-        if (mismatched > 0 && !opts.force) {
-            ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`${mismatched} note(s) are embedded under a different model than the active one (${provider.modelName})`));
-            ui.line(ui.dim("they are excluded from vector search until re-embedded"));
-            ui.line(ui.dim("run `vir embed --force` to re-embed the whole index"));
-        }
-        if (mismatched > 0 && opts.force) {
-            const estSecs = Math.max(1, Math.round(rows.length * 0.15));
-            ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`model boundary: re-embedding ${rows.length} note(s) under ${provider.modelName} (~${estSecs}s), replacing vectors from other models`));
-            if (!opts.yes) {
-                const rl = createInterface({ input: stdin, output: stdout });
-                const answer = (await rl.question("Proceed? [y/N] ")).trim().toLowerCase();
-                rl.close();
-                if (answer !== "y" && answer !== "yes") {
-                    ui.line(ui.dim("aborted — index unchanged"));
-                    return;
-                }
-            }
-        }
-        const existing = new Set(db
-            .getEmbeddings(root)
-            .filter((r) => r.embeddingModel === provider.modelName)
-            .map((r) => r.sessionId));
-        const target = opts.force
-            ? rows
-            : rows.filter((r) => !existing.has(r.sessionId));
-        // Topics live in their own table, so backfill them here too — a compose
-        // while Ollama was down heals on a manual `vir embed`, not only the next
-        // `vir run` sweep. --force re-embeds all topics; otherwise just NULL ones.
-        const topicTargets = opts.force
-            ? db.listTopics().map((t) => ({ id: t.id, content: t.content }))
-            : db.listTopicEmbeddingTargets();
-        // Articles live in their own table too — back-fill them here so a clip
-        // distilled while Ollama was down heals on a manual `vir embed`, not only
-        // the next `vir run` sweep. --force re-embeds all embeddable articles
-        // (keyed by source path); otherwise just the NULL-embedding ones.
-        const articleTargets = opts.force
-            ? db.listArticles().map((a) => ({ path: a.path, content: a.content }))
-            : db.listArticleEmbeddingTargets();
-        // PDFs live in their own table too — same back-fill rationale as articles.
-        const pdfTargets = opts.force
-            ? db.listPdfs().map((p) => ({ path: p.path, content: p.content }))
-            : db.listPdfEmbeddingTargets();
-        const total = target.length +
-            topicTargets.length +
-            articleTargets.length +
-            pdfTargets.length;
-        if (total === 0) {
-            ui.row(ui.success(ui.CHECK), ui.text("all notes already embedded"));
-            return;
-        }
-        const sp = ui.spinner(`embedding notes (0/${total})`).start();
-        let embedded = 0;
-        let skipped = 0;
-        let errors = 0;
-        for (let i = 0; i < target.length; i += 1) {
-            const r = target[i];
-            if (!r)
-                continue;
-            if (r.content.trim().length === 0) {
-                skipped += 1;
-                continue;
-            }
-            const vec = await embedNoteWithProvider(provider, r.content);
-            if (!vec) {
-                errors += 1;
-                continue;
-            }
-            db.storeEmbedding(r.sessionId, vec, provenance);
-            embedded += 1;
-            sp.text = ui.dim(`embedding notes (${embedded}/${total})`);
-        }
-        for (const t of topicTargets) {
-            if (!t.content || t.content.trim().length === 0) {
-                skipped += 1;
-                continue;
-            }
-            const vec = await embedNoteWithProvider(provider, t.content);
-            if (!vec) {
-                errors += 1;
-                continue;
-            }
-            db.storeTopicEmbedding(t.id, vec, provenance);
-            embedded += 1;
-            sp.text = ui.dim(`embedding notes (${embedded}/${total})`);
-        }
-        for (const a of articleTargets) {
-            if (!a.content || a.content.trim().length === 0) {
-                skipped += 1;
-                continue;
-            }
-            const vec = await embedNoteWithProvider(provider, a.content);
-            if (!vec) {
-                errors += 1;
-                continue;
-            }
-            db.storeArticleEmbedding(a.path, vec, provenance);
-            embedded += 1;
-            sp.text = ui.dim(`embedding notes (${embedded}/${total})`);
-        }
-        for (const p of pdfTargets) {
-            if (!p.content || p.content.trim().length === 0) {
-                skipped += 1;
-                continue;
-            }
-            const vec = await embedNoteWithProvider(provider, p.content);
-            if (!vec) {
-                errors += 1;
-                continue;
-            }
-            db.storePdfEmbedding(p.path, vec, provenance);
-            embedded += 1;
-            sp.text = ui.dim(`embedding notes (${embedded}/${total})`);
-        }
-        sp.succeed(ui.text(`embedded ${embedded} notes`));
-        ui.blank();
-        ui.divider();
-        ui.summary({
-            embedded: { value: embedded, color: ui.success },
-            skipped: { value: skipped, color: ui.muted },
-            errors: {
-                value: errors,
-                color: errors > 0 ? ui.errorColor : ui.dim,
-            },
-        });
-        ui.divider();
-    }
-    finally {
-        db.close();
-    }
-}));
+    .action(runAction(embedCommand));
 // JSON path for `vir query --json`: stdout gets a single JSON array on success
 // (`[]` when nothing matched), exit 0. On failure stdout stays EMPTY so the
 // plugin can `JSON.parse(stdout)` unguarded — the error goes to stderr as a
@@ -1094,88 +584,7 @@ program
     .option("--model <model>", "Synthesis model: haiku | sonnet")
     .option("--dry-run", "Show top sources + estimated cost, exit before LLM")
     .option("--yes", "Skip the cost confirmation prompt")
-    .action(runAction(async (topic, opts) => {
-    const cfg = loadConfig();
-    if (opts.model && !["haiku", "sonnet"].includes(opts.model)) {
-        console.error(chalk.red(`--model must be 'haiku' or 'sonnet', got '${opts.model}'`));
-        process.exitCode = 1;
-        return;
-    }
-    const limit = Math.min(50, Math.max(1, Number.parseInt(opts.limit ?? "20", 10) || 20));
-    const db = new StateDb();
-    try {
-        ui.header("compose");
-        ui.divider();
-        console.log(ui.text(topic));
-        ui.divider();
-        ui.blank();
-        const sp = ui.spinner("searching vault for related notes").start();
-        const sources = await gatherSources(cfg, db, topic, limit);
-        sp.stop();
-        if (sources.length === 0) {
-            ui.row(ui.warn(ui.WARN_GLYPH), ui.text("no related notes found — nothing to synthesize"));
-            ui.line(ui.dim("  run `vir run` to distill more sessions first"));
-            return;
-        }
-        for (const s of sources.slice(0, 10))
-            ui.sourceRow(s.title, s.score);
-        ui.divider();
-        const model = normalizeModelName(resolveModelShorthand(opts.model ?? cfg.models.distill), cfg.provider);
-        const { inputTokens, outputTokens } = estimateComposeCostTokens(topic, sources);
-        const estCost = estCostLabel(cfg, model, inputTokens, outputTokens);
-        ui.summary({
-            sources: { value: sources.length, color: ui.info },
-            model: { value: model, color: ui.accent },
-            "est. cost": { value: estCost, color: ui.warn },
-        });
-        ui.divider();
-        if (opts.dryRun) {
-            ui.line(ui.dim("  dry run — no synthesis performed; actuals may vary ±30%"));
-            return;
-        }
-        if (opts.yes !== true) {
-            const proceed = await confirm({
-                message: `synthesize with ${model} (~${estCost})?`,
-                default: true,
-            });
-            if (!proceed) {
-                ui.line(ui.dim("aborted"));
-                return;
-            }
-        }
-        const writer = new VaultWriter(cfg, db);
-        const sp2 = ui.spinner("synthesizing topic page").start();
-        let result;
-        try {
-            result = await composeFromSources(cfg, db, topic, sources, writer, {
-                forceModel: opts.model,
-            });
-            sp2.stop();
-        }
-        catch (err) {
-            sp2.fail(ui.errorColor(err.message));
-            process.exitCode = 1;
-            return;
-        }
-        ui.row(ui.success(ui.CHECK), ui.text(`wrote ${result.relPath}`));
-        ui.blank();
-        // Actual cost from the record callLLM just appended for this compose.
-        const rec = [...readCostLog()]
-            .reverse()
-            .find((r) => r.stage === "compose" && r.session === result.slug);
-        ui.summary({
-            title: { value: result.title, color: ui.text },
-            sources: { value: result.sourceCount, color: ui.info },
-            confidence: { value: result.confidence.toFixed(2), color: ui.info },
-            ...(rec && rec.estimated_cost_usd !== null
-                ? { cost: { value: ui.formatUsd(rec.estimated_cost_usd), color: ui.warn } }
-                : {}),
-        });
-    }
-    finally {
-        db.close();
-    }
-}));
+    .action(runAction(composeCommand));
 const projectsCmd = program
     .command("projects")
     .description("Per-project distillation decisions: table + include/exclude");
@@ -1299,7 +708,7 @@ program
     if (opts.approve !== undefined || opts.reject !== undefined) {
         throw new Error("--approve and --reject need --json (the terminal loop asks per note)");
     }
-    await runReview(opts);
+    await withPipelineLock(() => runReview(opts));
 }));
 program
     .command("audit")
@@ -1311,125 +720,7 @@ program
     .option("--dry-run", "Show notes, batches and est. cost, exit before any LLM call")
     .option("--yes", "Skip the cost confirmation prompt")
     .option("--apply-rejects", "Move notes with a fresh reject verdict to .rejected/ (no model call; undo with vir review --restore)")
-    .action(runAction(async (opts) => {
-    const limit = parseLimitOption(opts.limit);
-    if (limit === null) {
-        ui.header("audit");
-        ui.blank();
-        ui.row(ui.errorColor(ui.CROSS), ui.text(`--limit must be a positive integer, got "${opts.limit}"`));
-        process.exitCode = 1;
-        return;
-    }
-    const cfg = loadConfig();
-    const db = new StateDb();
-    try {
-        const root = vaultRoot(cfg);
-        if (opts.applyRejects) {
-            const { toMove: targets, verified } = previewRejects(db.listDistilled(), db.listAudits(), (r) => noteIsVerified(root, r), opts.project);
-            ui.header("audit");
-            ui.blank();
-            ui.summary({
-                rejects: { value: targets.length, color: ui.errorColor },
-                "approved, skipped": { value: verified.length, color: verified.length > 0 ? ui.warn : ui.muted },
-            });
-            for (const r of targets.slice(0, 20))
-                ui.line(`  ${ui.dim(ui.BULLET)} ${ui.text(r.topic)} ${ui.dim(r.project)}`);
-            if (targets.length > 20)
-                ui.line(ui.dim(`  … and ${targets.length - 20} more`));
-            ui.divider();
-            if (targets.length === 0 || opts.dryRun) {
-                if (opts.dryRun)
-                    ui.line(ui.dim("  dry run — nothing moved"));
-                return;
-            }
-            if (opts.yes !== true) {
-                const proceed = await confirm({ message: `move ${targets.length} notes to .rejected/?`, default: false });
-                if (!proceed) {
-                    ui.line(ui.dim("aborted"));
-                    return;
-                }
-            }
-            const s = applyAuditRejects(db, root, { project: opts.project });
-            ui.summary({
-                moved: { value: s.moved, color: ui.info },
-                "missing file": { value: s.missingFile, color: ui.muted },
-                collision: { value: s.collision, color: s.collision > 0 ? ui.warn : ui.muted },
-                verified: { value: s.verified, color: s.verified > 0 ? ui.warn : ui.muted },
-            });
-            ui.line(ui.dim("  undo any of them with `vir review --restore <note>`"));
-            return;
-        }
-        const auditOpts = { project: opts.project, limit, all: opts.all };
-        const isVerified = (r) => noteIsVerified(root, r);
-        const model = normalizeModelName(resolveModelShorthand(opts.model ?? cfg.models.distill), cfg.provider);
-        const picked = selectAuditRows(db.listDistilled(), db.listAudits(), auditOpts, isVerified);
-        const batches = batchByProject(picked.rows);
-        const inputTokens = Math.ceil(picked.rows.reduce((n, r) => n + r.content.length, 0) / 4 + batches.length * 600);
-        const outputTokens = picked.rows.length * 60;
-        const estCost = estCostLabel(cfg, model, inputTokens, outputTokens);
-        ui.header("audit");
-        ui.blank();
-        ui.summary({
-            notes: { value: picked.rows.length, color: ui.info },
-            batches: { value: batches.length, color: ui.info },
-            "already audited": { value: picked.skippedFresh, color: ui.muted },
-            verified: { value: picked.skippedVerified, color: ui.muted },
-            model: { value: model, color: ui.accent },
-            "est. cost": { value: estCost, color: ui.warn },
-        });
-        ui.divider();
-        if (picked.rows.length === 0) {
-            ui.row(ui.success(ui.CHECK), ui.text("nothing to audit"));
-            return;
-        }
-        if (opts.dryRun) {
-            ui.line(ui.dim("  dry run — no model calls made"));
-            return;
-        }
-        if (opts.yes !== true) {
-            const proceed = await confirm({ message: `audit ${picked.rows.length} notes with ${model} (~${estCost})?`, default: true });
-            if (!proceed) {
-                ui.line(ui.dim("aborted"));
-                return;
-            }
-        }
-        const client = maybeAnthropicClient(cfg);
-        const sp = ui.spinner(`auditing ${batches.length} batches`).start();
-        let summary;
-        try {
-            summary = await runAudit(db, auditOpts, {
-                isVerified,
-                llm: (prompt) => withRateLimitRetry(() => callLLM(cfg, client, {
-                    prompt,
-                    model,
-                    maxTokens: 4000,
-                    cost: { stage: "audit" },
-                })),
-            });
-            sp.stop();
-        }
-        catch (err) {
-            sp.fail(ui.errorColor(err.message));
-            process.exitCode = 1;
-            return;
-        }
-        ui.summary({
-            audited: { value: summary.audited, color: ui.info },
-            keep: { value: summary.byVerdict.keep, color: ui.success },
-            verify: { value: summary.byVerdict.verify, color: ui.warn },
-            merge: { value: summary.byVerdict.merge, color: ui.warn },
-            reject: { value: summary.byVerdict.reject, color: ui.errorColor },
-            unanswered: { value: summary.unanswered, color: ui.muted },
-            "failed batches": { value: summary.failedBatches, color: summary.failedBatches > 0 ? ui.errorColor : ui.muted },
-        });
-        ui.line(ui.dim("  nothing was moved — walk the flagged notes with `vir review --audited`"));
-        if (summary.failedBatches > 0)
-            process.exitCode = 1;
-    }
-    finally {
-        db.close();
-    }
-}));
+    .action(runAction(auditCommand));
 program
     .command("prune")
     .description("Demote agent-derived notes to .rejected/ (dry run by default)")
@@ -1585,342 +876,6 @@ function renderDaemon(ds, cadenceHours) {
         `${ui.dim("config")}   ${ui.muted(ds.configPath ? collapseHome(ds.configPath) : "—")}`,
     ], { title: "daemon", width: 52 });
 }
-async function cmdInit() {
-    ensureVirDir();
-    const existing = configExists() ? safeLoad() : null;
-    ui.header("init");
-    ui.blank();
-    // ── vault path ──────────────────────────────────────────────────────────
-    let vaultPath = "";
-    for (;;) {
-        vaultPath = await input({
-            message: "Obsidian vault path",
-            default: existing?.vaultPath ??
-                join(homedir(), "Documents", "Obsidian", "MyVault"),
-        });
-        const expanded = expandHome(vaultPath);
-        if (existsSync(expanded))
-            break;
-        const create = await confirm({
-            message: `Vault path does not exist (${expanded}). Create it?`,
-            default: true,
-        });
-        if (create) {
-            try {
-                mkdirSync(expanded, { recursive: true });
-                break;
-            }
-            catch (err) {
-                console.error(chalk.red(`failed to create: ${err.message}`));
-            }
-        }
-    }
-    const outputDir = await input({
-        message: "Output subdir inside vault",
-        default: existing?.outputDir ?? "vir",
-    });
-    // ── claude projects dir ─────────────────────────────────────────────────
-    let claudeProjectsDir = "";
-    for (;;) {
-        claudeProjectsDir = await input({
-            message: "Claude Code projects dir",
-            default: existing?.claudeProjectsDir ?? join(homedir(), ".claude", "projects"),
-        });
-        const expanded = expandHome(claudeProjectsDir);
-        if (existsSync(expanded))
-            break;
-        console.warn(chalk.yellow("directory not found — Claude Code sessions may not exist yet"));
-        const cont = await confirm({
-            message: "continue anyway?",
-            default: false,
-        });
-        if (cont)
-            break;
-    }
-    // ── web articles (optional second input source) ─────────────────────────
-    let articlesDir = existing?.articlesDir;
-    const wantsArticles = await confirm({
-        message: "Do you save web articles to a folder (e.g. Obsidian Web Clipper)?",
-        default: existing?.articlesDir !== undefined,
-    });
-    if (wantsArticles) {
-        for (;;) {
-            articlesDir = await input({
-                message: "Articles (raw/) directory",
-                default: existing?.articlesDir ??
-                    join(homedir(), "Documents", "Obsidian", "raw"),
-            });
-            const expanded = expandHome(articlesDir);
-            if (existsSync(expanded))
-                break;
-            const create = await confirm({
-                message: `Path does not exist (${expanded}). Create it?`,
-                default: true,
-            });
-            if (create) {
-                try {
-                    mkdirSync(expanded, { recursive: true });
-                    break;
-                }
-                catch (err) {
-                    console.error(chalk.red(`failed to create: ${err.message}`));
-                }
-            }
-            else {
-                break;
-            }
-        }
-    }
-    else {
-        articlesDir = undefined;
-    }
-    // ── PDFs / papers (optional third input source) ──────────────────────────
-    let pdfsDir = existing?.pdfsDir;
-    const wantsPdfs = await confirm({
-        message: "Do you keep PDFs / papers in a folder to ingest?",
-        default: existing?.pdfsDir !== undefined,
-    });
-    if (wantsPdfs) {
-        for (;;) {
-            pdfsDir = await input({
-                message: "PDFs directory",
-                default: existing?.pdfsDir ?? join(homedir(), "Documents", "papers"),
-            });
-            const expanded = expandHome(pdfsDir);
-            if (existsSync(expanded))
-                break;
-            const create = await confirm({
-                message: `Path does not exist (${expanded}). Create it?`,
-                default: true,
-            });
-            if (create) {
-                try {
-                    mkdirSync(expanded, { recursive: true });
-                    break;
-                }
-                catch (err) {
-                    console.error(chalk.red(`failed to create: ${err.message}`));
-                }
-            }
-            else {
-                break;
-            }
-        }
-    }
-    else {
-        pdfsDir = undefined;
-    }
-    const cadenceHours = Number(await input({
-        message: "Cadence (hours)",
-        default: String(existing?.cadenceHours ?? 3),
-        validate: (v) => {
-            const n = Number(v);
-            return Number.isFinite(n) && n > 0 ? true : "must be a positive number";
-        },
-    }));
-    // ── provider picker ─────────────────────────────────────────────────────
-    const provider = (await select({
-        message: "Provider",
-        default: existing?.provider ?? "anthropic",
-        choices: [
-            {
-                name: "Anthropic    (API key — predictable per-session cost, no effect on your Claude Code limits)",
-                value: "anthropic",
-            },
-            {
-                name: "Claude Code  (subscription — free and keyless; distills consume your Claude Code usage limits)",
-                value: "claude-cli",
-            },
-            {
-                name: "Kie.ai       (~72% cheaper API, third-party proxy — you trade reliability for cost)",
-                value: "kie",
-            },
-        ],
-    }));
-    // Secret prompt discipline: mask while typing, echo only a masked
-    // confirmation (maskSecret), and NEVER render the existing key as the
-    // visible inquirer default — that prints the full secret to the terminal
-    // before a single keystroke. Empty input keeps the existing/env key.
-    const promptSecret = async (message, keep, validate) => {
-        const value = await input({
-            message: keep
-                ? `${message} (Enter keeps ${maskSecret(keep)})`
-                : message,
-            transformer: (v, { isFinal }) => isFinal ? maskSecret(v || keep || "") : "•".repeat(v.length),
-            validate: (v) => (v === "" && keep ? true : validate(v)),
-        });
-        return value === "" && keep ? keep : value;
-    };
-    let anthropicApiKey;
-    let kieApiKey;
-    if (provider === "anthropic") {
-        anthropicApiKey = await promptSecret("Anthropic API key", existing?.anthropicApiKey ?? process.env.ANTHROPIC_API_KEY ?? undefined, (v) => (v.startsWith("sk-ant-") ? true : "key should start with sk-ant-"));
-    }
-    else if (provider === "kie") {
-        kieApiKey = await promptSecret("Kie.ai API key", existing?.kieApiKey ?? process.env.KIE_API_KEY ?? undefined, (v) => (v.length > 10 ? true : "enter a valid Kie.ai API key"));
-    }
-    // claude-cli: no credential of any kind — it uses the `claude` login.
-    // ── model pickers (provider-aware) ──────────────────────────────────────
-    // claude-cli accepts the same full Anthropic model ids (and pins them per
-    // invocation via --model), so it shares the anthropic id set.
-    const classifyChoices = provider !== "kie"
-        ? [
-            {
-                name: "claude-haiku-4-5-20251001  (recommended)",
-                value: "claude-haiku-4-5-20251001",
-            },
-            { name: "claude-sonnet-4-6", value: "claude-sonnet-4-6" },
-        ]
-        : [
-            {
-                name: "claude-haiku-4-5  (recommended)",
-                value: "claude-haiku-4-5",
-            },
-            { name: "claude-sonnet-4-6", value: "claude-sonnet-4-6" },
-        ];
-    const classifyModel = await select({
-        message: "Classify model (fast pass)",
-        choices: classifyChoices,
-    });
-    const distillChoices = provider !== "kie"
-        ? [
-            {
-                name: "claude-sonnet-5  (recommended)",
-                value: "claude-sonnet-5",
-            },
-            { name: "claude-sonnet-4-6", value: "claude-sonnet-4-6" },
-            {
-                name: "claude-haiku-4-5-20251001  (faster, cheaper)",
-                value: "claude-haiku-4-5-20251001",
-            },
-        ]
-        : [
-            {
-                name: "claude-sonnet-4-6  (recommended)",
-                value: "claude-sonnet-4-6",
-            },
-            {
-                name: "claude-haiku-4-5  (faster, cheaper)",
-                value: "claude-haiku-4-5",
-            },
-        ];
-    const distillModel = await select({
-        message: "Distill model (deep extraction)",
-        choices: distillChoices,
-    });
-    const filterThreshold = Number(await input({
-        message: "Filter threshold (0..1)",
-        default: String(existing?.filterThreshold ?? 0.4),
-        validate: (v) => {
-            const n = Number(v);
-            return Number.isFinite(n) && n >= 0 && n <= 1
-                ? true
-                : "must be between 0 and 1";
-        },
-    }));
-    // ── project triage (the primary decision point) ─────────────────────────
-    // Every project found under the Claude projects dir is shown once with its
-    // session count and rough cost; selected = include, unselected = exclude.
-    // Projects that appear later start undecided and trigger the run prompt.
-    let projectDecisions = {};
-    let agentTranscriptsAnswer;
-    try {
-        const projectsDirX = expandHome(claudeProjectsDir);
-        const allFound = scanSessions(projectsDirX);
-        // Triage counts + the agent-transcript question. Only top-level
-        // transcripts count (nested workflow/sidechain have their own filter),
-        // and agent transcripts are excluded from the per-project multi-select
-        // numbers so the costs shown reflect what would actually distill.
-        const topLevel = allFound.filter((s) => classifyTranscript(s.path, projectsDirX) === "session");
-        const counts = { interactive: 0, agent: 0, stub: 0 };
-        const agentPaths = new Set();
-        for (const s of topLevel) {
-            const cat = categorizeTranscriptHead(readTranscriptHead(s.path), s.size);
-            counts[cat] += 1;
-            if (cat === "agent")
-                agentPaths.add(s.path);
-        }
-        if (counts.agent > 0) {
-            ui.blank();
-            ui.line(ui.dim(`  ${counts.interactive} interactive · ${counts.agent} SDK-launched · ${counts.stub} stubs`));
-            agentTranscriptsAnswer = (await select({
-                message: "SDK-launched agent transcripts (review/verify harness output) — distill them?",
-                default: existing?.agentTranscripts ?? "exclude",
-                choices: [
-                    {
-                        name: "Exclude  (recommended — agent-internal execution, not your decisions)",
-                        value: "exclude",
-                    },
-                    { name: "Include  (distill them like any session)", value: "include" },
-                ],
-            }));
-        }
-        const found = agentTranscriptsAnswer !== "include"
-            ? topLevel.filter((s) => !agentPaths.has(s.path))
-            : topLevel;
-        const groups = [...groupByProject(found, projectsDirX).values()];
-        if (groups.length > 0) {
-            const classifyId = normalizeModelName(classifyModel, provider);
-            const distillId = normalizeModelName(distillModel, provider);
-            const infos = groups
-                .map((g) => ({
-                name: g.name,
-                sessionCount: g.sessions.length,
-                totalBytes: g.totalBytes,
-                estCost: g.sessions.reduce((sum, s) => sum +
-                    estimateSessionCost(provider, classifyId, distillId, s.size), 0),
-            }))
-                .sort((a, b) => b.estCost - a.estCost);
-            ui.blank();
-            ui.line(ui.dim("  Which projects should vir distill? Costs are rough upper bounds."));
-            projectDecisions = await promptProjectDecisions(infos, existing?.projects ?? {}, "Projects to track");
-        }
-    }
-    catch (err) {
-        console.warn(chalk.yellow(`project scan failed (${err.message}) — you can decide later with vir projects`));
-    }
-    const parsed = ConfigSchema.safeParse(buildInitConfig(existing, {
-        vaultPath,
-        outputDir,
-        claudeProjectsDir,
-        cadenceHours,
-        provider,
-        anthropicApiKey,
-        kieApiKey,
-        filterThreshold,
-        articlesDir,
-        pdfsDir,
-        classifyModel,
-        distillModel,
-        projects: projectDecisions,
-        agentTranscripts: agentTranscriptsAnswer,
-    }));
-    if (!parsed.success) {
-        console.error(chalk.red("invalid config:"));
-        for (const issue of parsed.error.issues) {
-            console.error(`  - ${issue.path.join(".")}: ${issue.message}`);
-        }
-        process.exitCode = 1;
-        return;
-    }
-    saveConfig(parsed.data);
-    ui.blank();
-    ui.row(ui.success(ui.CHECK), ui.text(`saved ${CONFIG_PATH}`));
-    ui.blank();
-    const wantsMcp = await confirm({
-        message: "Register Vir with Claude Code now? (recommended)",
-        default: true,
-    });
-    if (wantsMcp) {
-        await installToClaudeCode("user");
-    }
-    if (process.platform === "darwin" && parsed.data.notifications) {
-        ui.blank();
-        setupNotifications({ test: false });
-    }
-    ui.blank();
-    ui.line(ui.dim("next: `vir run` to test once, then `vir schedule install`"));
-}
 function renderPlan(p) {
     const title = collapseHome(p.target);
     if (!p.exists) {
@@ -1948,25 +903,6 @@ function collapseHome(p) {
     const h = homedir();
     return p.startsWith(h) ? "~" + p.slice(h.length) : p;
 }
-function noteRefOf(r) {
-    const dir = `${r.category}s`;
-    const slug = r.topic
-        .toLowerCase()
-        .replace(/[^a-z0-9]+/g, "-")
-        .replace(/^-+|-+$/g, "");
-    return `${dir}/${slug}-${r.sessionId.slice(0, 8)}`;
-}
-function preview(s) {
-    return s.replace(/\s+/g, " ").trim().slice(0, 80);
-}
-function safeLoad() {
-    try {
-        return loadConfig();
-    }
-    catch {
-        return null;
-    }
-}
 // Safety net for anything that escapes the per-action `runAction` wrapper (e.g.
 // commander-internal rejections before the action handler is reached). Set
 // `process.exitCode` instead of calling `process.exit` so buffered stdout/stderr