@djolex999/vir-cli 0.17.1 → 0.18.1

package/README.md

@@ -22,7 +22,7 @@ developer-tools, mcp, local-first, cross-platform, llm-wiki
   <a href="https://www.npmjs.com/package/@djolex999/vir-cli"><img src="https://img.shields.io/npm/v/@djolex999/vir-cli?color=7c6af7&label=npm" alt="npm version"></a>
   <a href="https://www.npmjs.com/package/@djolex999/vir-cli"><img src="https://img.shields.io/npm/dw/@djolex999/vir-cli?color=4fd1a0" alt="npm downloads"></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-22d3ee" alt="license"></a>
-  <a href="#project-status"><img src="https://img.shields.io/badge/tests-534%20passing-22c55e" alt="tests"></a>
+  <a href="#project-status"><img src="https://img.shields.io/badge/tests-610%20passing-22c55e" alt="tests"></a>
   <a href="#project-status"><img src="https://img.shields.io/badge/platforms-macOS%20%7C%20Linux-lightgrey" alt="platforms"></a>
   <a href="https://modelcontextprotocol.io"><img src="https://img.shields.io/badge/MCP-server-c084fc" alt="mcp"></a>
   <a href="#"><img src="https://img.shields.io/badge/local--first-yes-f59e0b" alt="local-first"></a>
@@ -362,6 +362,10 @@ with your distro, init system, and Node version.
 | `vir lint`                  | cheap | Find orphans, stale notes, contradictions |
 | `vir dedupe`                | cheap | Interactive duplicate detection + merge   |
 | `vir review`                | free  | Walk new notes: approve/edit/reject       |
+| `vir lint --strays`         | free  | Note files with no live DB row (retitle debris) |
+| `vir prune`                 | free  | Dry run: agent-derived notes to demote    |
+| `vir prune --apply`         | free  | Demote them to `.rejected/` (never deletes) |
+| `vir prune --restore`       | free  | Put every pruned note back, exactly       |
 | `vir sync-claude`           | free  | Inject top knowledge into CLAUDE.md       |
 | `vir embed`                 | free  | Generate embeddings for semantic search   |
 | `vir embed --setup`         | free  | Install the local embedding provider (no Ollama needed) |
@@ -504,8 +508,8 @@ improvements. Delete it any time; disable it with `"logQueries": false` in
 
 |                |                                           |
 | -------------- | ----------------------------------------- |
-| Version        | 0.17.1                                    |
-| Tests          | 534 passing                               |
+| Version        | 0.18.1                                    |
+| Tests          | 610 passing                               |
 | Platforms      | macOS (launchd), Linux (systemd/cron)     |
 | Node           | 20+                                       |
 | First-run cost | $1 to $5 (Kie.ai optional, ~72% cheaper)  |

package/dist/claude/updater.js

@@ -193,32 +193,93 @@ function computeDiff(old, next) {
     }
     return { added, removed, upgraded, unchanged };
 }
+// Marker offsets that are REAL — i.e. not inside a fenced code block. A
+// CLAUDE.md may legitimately document vir's own markers (this repo's docs do),
+// and editing the file at an example would corrupt it.
+function markerOffsets(raw) {
+    const starts = [];
+    const ends = [];
+    let offset = 0;
+    let fenced = false;
+    for (const line of raw.split("\n")) {
+        const t = line.trim();
+        if (t.startsWith("```") || t.startsWith("~~~")) {
+            fenced = !fenced;
+        }
+        else if (!fenced) {
+            if (t === VIR_START)
+                starts.push(offset);
+            else if (t === VIR_END)
+                ends.push(offset);
+        }
+        offset += line.length + 1;
+    }
+    return { starts, ends };
+}
+// Pair markers into complete blocks, walking forward: a START claims the first
+// END after it. Returns null when anything is left unmatched — an orphan START
+// from a hand-edit, or an END before any START.
+function pairBlocks(starts, ends) {
+    const blocks = [];
+    let ei = 0;
+    for (const start of starts) {
+        while (ei < ends.length && ends[ei] < start)
+            return null; // END before START
+        if (ei >= ends.length)
+            return null; // START with no END after it
+        blocks.push({ from: start, to: ends[ei] + VIR_END.length });
+        ei += 1;
+    }
+    if (ei !== ends.length)
+        return null; // trailing unmatched END
+    return blocks;
+}
 export function applyPlan(plan) {
     if (!plan.exists)
-        return false;
+        return { ok: false, reason: "file does not exist" };
     let raw;
     try {
         raw = readFileSync(plan.target, "utf8");
     }
     catch {
-        return false;
+        return { ok: false, reason: "could not read file" };
     }
+    const { starts, ends } = markerOffsets(raw);
     let updated;
-    if (raw.includes(VIR_START) && raw.includes(VIR_END)) {
-        const start = raw.indexOf(VIR_START);
-        const end = raw.indexOf(VIR_END) + VIR_END.length;
-        updated = raw.slice(0, start) + plan.newBlock + raw.slice(end);
-    }
-    else {
+    if (starts.length === 0 && ends.length === 0) {
         const sep = raw.endsWith("\n") ? "\n" : "\n\n";
         updated = raw + sep + plan.newBlock + "\n";
     }
+    else {
+        const blocks = pairBlocks(starts, ends);
+        // Unbalanced markers mean a hand-edit went wrong. Appending here is what
+        // made this destructive: the NEXT sync would slice from the orphan marker
+        // to the appended block's END and delete everything the user wrote in
+        // between. Refuse, say so, and let them fix their own file.
+        if (blocks === null || blocks.length === 0) {
+            return {
+                ok: false,
+                reason: `unbalanced ${VIR_START} / ${VIR_END} markers — fix them by hand, nothing was written`,
+            };
+        }
+        // Replace the first block; drop any later ones. Splice back-to-front so
+        // earlier offsets stay valid. Later blocks are entirely vir-owned, so
+        // removing them takes none of the user's content.
+        updated = raw;
+        for (let i = blocks.length - 1; i >= 1; i -= 1) {
+            const b = blocks[i];
+            updated = updated.slice(0, b.from) + updated.slice(b.to);
+        }
+        const first = blocks[0];
+        updated =
+            updated.slice(0, first.from) + plan.newBlock + updated.slice(first.to);
+    }
     try {
         writeFileSync(plan.target, updated);
-        return true;
+        return { ok: true };
     }
     catch {
-        return false;
+        return { ok: false, reason: "could not write file" };
     }
 }
 export function globalClaudePath() {

package/dist/claude/updater.js.map

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package/dist/cli/pruneAction.js

@@ -0,0 +1,88 @@
+import { loadConfig } from "../config.js";
+import { applyPrunePlan, buildPrunePlan, restorePruned, } from "../prune/prune.js";
+import { StateDb } from "../state/db.js";
+import * as ui from "../ui/display.js";
+function renderPlan(plan) {
+    ui.header("prune — agent-derived notes");
+    ui.blank();
+    const reasons = Object.entries(plan.byReason).sort((a, b) => b[1] - a[1]);
+    if (reasons.length === 0) {
+        ui.row(ui.success(ui.CHECK), ui.text("nothing to prune"));
+    }
+    else {
+        for (const [reason, n] of reasons) {
+            ui.row(ui.warn(ui.DIAMOND), ui.text(reason), ui.dim(String(n)));
+        }
+    }
+    ui.blank();
+    ui.line(ui.dim("  kept:"));
+    for (const [reason, n] of Object.entries(plan.byKeepReason).sort((a, b) => b[1] - a[1])) {
+        // The two report-only buckets are the honest part of this command: no
+        // evidence exists to judge them, so they are never touched.
+        const note = reason === "unclassifiable"
+            ? " (no entrypoint, transcript gone — never pruned)"
+            : reason === "merge-winner"
+                ? " (merge parentage unknown — never pruned)"
+                : "";
+        ui.line(ui.dim(`    ${reason}: ${n}${note}`));
+    }
+    ui.blank();
+    ui.divider();
+    ui.summary({
+        "would prune": { value: plan.prune.length, color: ui.warn },
+        keep: { value: plan.keep.length, color: ui.info },
+        "already pruned": { value: plan.alreadyPruned, color: ui.dim },
+        "dangling links": {
+            value: plan.danglingLinks,
+            color: plan.danglingLinks > 0 ? ui.warn : ui.dim,
+        },
+    });
+    ui.divider();
+    if (plan.danglingLinks > 0) {
+        ui.line(ui.dim(`  ${plan.danglingLinks} wikilink(s) in kept notes point at a pruned note — reported, not rewritten`));
+    }
+}
+export async function pruneCommand(opts) {
+    const cfg = await loadConfig();
+    const db = new StateDb();
+    try {
+        if (opts.restore === true) {
+            const res = restorePruned(db, cfg);
+            ui.header("prune --restore");
+            ui.blank();
+            ui.summary({
+                restored: { value: res.restored, color: ui.success },
+                "file missing": {
+                    value: res.missing,
+                    color: res.missing > 0 ? ui.warn : ui.dim,
+                },
+            });
+            return;
+        }
+        const plan = buildPrunePlan(db, cfg);
+        renderPlan(plan);
+        // Dry run is the default: this command demotes a chunk of the vault, so
+        // the destructive-looking path has to be the one you ask for by name.
+        if (opts.apply !== true) {
+            ui.blank();
+            ui.line(ui.dim("  dry run — nothing moved, nothing written"));
+            ui.line(ui.dim("  run `vir prune --apply` to demote, `--restore` to undo"));
+            return;
+        }
+        const res = applyPrunePlan(db, cfg, plan);
+        ui.blank();
+        ui.summary({
+            "notes moved": { value: res.moved, color: ui.success },
+            "rows marked": { value: res.marked, color: ui.success },
+            "state only": {
+                value: res.stateOnly,
+                color: res.stateOnly > 0 ? ui.warn : ui.dim,
+            },
+        });
+        ui.line(ui.dim("  demoted to .rejected/ — `vir prune --restore` puts them back"));
+    }
+    finally {
+        db.close();
+    }
+}
+//# sourceMappingURL=pruneAction.js.map

package/dist/cli/pruneAction.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pruneAction.js","sourceRoot":"","sources":["../../src/cli/pruneAction.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAC1C,OAAO,EACL,cAAc,EACd,cAAc,EACd,aAAa,GAEd,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAC;AACzC,OAAO,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAQvC,SAAS,UAAU,CAAC,IAAe;IACjC,EAAE,CAAC,MAAM,CAAC,6BAA6B,CAAC,CAAC;IACzC,EAAE,CAAC,KAAK,EAAE,CAAC;IAEX,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1E,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,CAAC;IAC5D,CAAC;SAAM,CAAC;QACN,KAAK,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,OAAO,EAAE,CAAC;YAClC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAClE,CAAC;IACH,CAAC;IAED,EAAE,CAAC,KAAK,EAAE,CAAC;IACX,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC;IAC3B,KAAK,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,IAAI,CAC9D,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CACtB,EAAE,CAAC;QACF,sEAAsE;QACtE,4DAA4D;QAC5D,MAAM,IAAI,GACR,MAAM,KAAK,gBAAgB;YACzB,CAAC,CAAC,kDAAkD;YACpD,CAAC,CAAC,MAAM,KAAK,cAAc;gBACzB,CAAC,CAAC,2CAA2C;gBAC7C,CAAC,CAAC,EAAE,CAAC;QACX,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,MAAM,KAAK,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC,CAAC;IAChD,CAAC;IAED,EAAE,CAAC,KAAK,EAAE,CAAC;IACX,EAAE,CAAC,OAAO,EAAE,CAAC;IACb,EAAE,CAAC,OAAO,CAAC;QACT,aAAa,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,IAAI,EAAE;QAC3D,IAAI,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,IAAI,EAAE;QACjD,gBAAgB,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,aAAa,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE;QAC9D,gBAAgB,EAAE;YAChB,KAAK,EAAE,IAAI,CAAC,aAAa;YACzB,KAAK,EAAE,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG;SACjD;KACF,CAAC,CAAC;IACH,EAAE,CAAC,OAAO,EAAE,CAAC;IACb,IAAI,IAAI,CAAC,aAAa,GAAG,CAAC,EAAE,CAAC;QAC3B,EAAE,CAAC,IAAI,CACL,EAAE,CAAC,GAAG,CACJ,KAAK,IAAI,CAAC,aAAa,6EAA6E,CACrG,CACF,CAAC;IACJ,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,IAAqB;IACtD,MAAM,GAAG,GAAG,MAAM,UAAU,EAAE,CAAC;IAC/B,MAAM,EAAE,GAAG,IAAI,OAAO,EAAE,CAAC;IACzB,IAAI,CAAC;QACH,IAAI,IAAI,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;YAC1B,MAAM,GAAG,GAAG,aAAa,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC;YACnC,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC;YAC7B,EAAE,CAAC,KAAK,EAAE,CAAC;YACX,EAAE,CAAC,OAAO,CAAC;gBACT,QAAQ,EAAE,EAAE,KAAK,EAAE,GAAG,CAAC,QAAQ,EAAE,KAAK,EAAE,EAAE,CAAC,OAAO,EAAE;gBACpD,cAAc,EAAE;oBACd,KAAK,EAAE,GAAG,CAAC,OAAO;oBAClB,KAAK,EAAE,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG;iBAC1C;aACF,CAAC,CAAC;YACH,OAAO;QACT,CAAC;QAED,MAAM,IAAI,GAAG,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC;QACrC,UAAU,CAAC,IAAI,CAAC,CAAC;QAEjB,wEAAwE;QACxE,sEAAsE;QACtE,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE,CAAC;YACxB,EAAE,CAAC,KAAK,EAAE,CAAC;YACX,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,CAAC,4CAA4C,CAAC,CAAC,CAAC;YAC9D,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,CAAC,0DAA0D,CAAC,CAAC,CAAC;YAC5E,OAAO;QACT,CAAC;QAED,MAAM,GAAG,GAAG,cAAc,CAAC,EAAE,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC;QAC1C,EAAE,CAAC,KAAK,EAAE,CAAC;QACX,EAAE,CAAC,OAAO,CAAC;YACT,aAAa,EAAE,EAAE,KAAK,EAAE,GAAG,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,OAAO,EAAE;YACtD,aAAa,EAAE,EAAE,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,OAAO,EAAE;YACvD,YAAY,EAAE;gBACZ,KAAK,EAAE,GAAG,CAAC,SAAS;gBACpB,KAAK,EAAE,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG;aAC5C;SACF,CAAC,CAAC;QACH,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,GAAG,CAAC,gEAAgE,CAAC,CAAC,CAAC;IACpF,CAAC;YAAS,CAAC;QACT,EAAE,CAAC,KAAK,EAAE,CAAC;IACb,CAAC;AACH,CAAC"}

package/dist/cli/reconcile.js

@@ -37,6 +37,16 @@ export function selectReconcileTargets(rows, force = false) {
             (r.error !== null && r.error !== "")) &&
         (force || (r.attempts ?? 0) < MAX_DISTILL_ATTEMPTS));
 }
+// A target whose transcript is gone can't be retried. If an earlier good
+// distill survives (the orphan shape: error set, content kept), the stale
+// error is the only thing hiding that note from listDistilled — clear it.
+// Must run BEFORE any missing-file skip, or the orphan is stranded forever.
+export function handleMissingSource(t, clearError) {
+    if (t.content === null || t.content === "")
+        return "missing";
+    clearError(t.path);
+    return "restored";
+}
 // Build the per-target summary (cost estimate + collateral flag) without doing
 // any network work. Used by both the dry-run report and the live confirmation.
 export function summarizeReconcileTargets(cfg, targets, costSessionIds, forceDistillModel) {
@@ -160,28 +170,20 @@ export async function runReconcile(cfg, opts = {}) {
         let missingFile = 0;
         for (const t of targets) {
             if (!existsSync(t.path)) {
-                missingFile += 1;
-                ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`missing on disk — skipped: ${t.path.slice(-60)}`));
+                if (handleMissingSource(t, (p) => db.clearError(p)) === "restored") {
+                    recovered += 1;
+                    ui.row(ui.success(ui.CHECK), ui.text("source gone — restored last good note"));
+                }
+                else {
+                    missingFile += 1;
+                    ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`missing on disk — skipped: ${t.path.slice(-60)}`));
+                }
                 continue;
             }
             // Bypass the SHA-256 processed-cache check intentionally — these rows
             // are cached but we know their stored content is empty, so we want a
             // forced retry. Parse, score, distill, then update the row in place.
             try {
-                if (!existsSync(t.path)) {
-                    if (t.content !== null && t.content !== "") {
-                        // Source transcript is gone; the previous good distill is all
-                        // that's left. Clear the stale error so the note resurfaces in
-                        // listDistilled instead of staying hidden forever.
-                        db.clearError(t.path);
-                        recovered += 1;
-                        ui.row(ui.success(ui.CHECK), ui.text("source gone — restored last good note"));
-                        continue;
-                    }
-                    stillFailed += 1;
-                    ui.row(ui.errorColor(ui.CROSS), ui.text("source transcript missing — nothing to recover"));
-                    continue;
-                }
                 const parsed = parseSession(t.path, t.hash);
                 const score = scoreSession(parsed, cfg.filterThreshold);
                 if (!score.passes) {

package/dist/cli/reconcile.js.map

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package/dist/cli/review.js

@@ -4,12 +4,11 @@ import { basename, join } from "node:path";
 import { stdin, stdout } from "node:process";
 import { createInterface } from "node:readline/promises";
 import { loadConfig } from "../config.js";
-import { kebab } from "../pipeline/writer.js";
+import { REJECTED_DIR, kebab } from "../pipeline/writer.js";
 import * as ui from "../ui/display.js";
 // The four typed category dirs hold reviewable notes. `.rejected/`, `archived/`,
 // `projects/`, index.md and log.md are intentionally never walked.
 const CATEGORY_DIRS = ["patterns", "gotchas", "decisions", "tools"];
-const REJECTED_DIR = ".rejected";
 // Frontmatter is line-oriented `key: value`. Mirrors mcp/server.ts so review
 // reads notes the same way the rest of the codebase does — strips surrounding
 // quotes so a value like `topic: "x"` parses to `x`.

package/dist/cli/review.js.map

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

@@ -12,9 +12,11 @@ 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 { applyPlan, planUpdates } from "./claude/updater.js";
+import { pruneCommand } from "./cli/pruneAction.js";
 import { detectDuplicates } from "./dedupe/detector.js";
 import { mergeNotes } from "./dedupe/merger.js";
 import { contradictionCheck, orphanCheck, stalenessCheck, } from "./lint/linter.js";
+import { strayFileCheck } from "./lint/strayFiles.js";
 import { runPipeline } from "./pipeline/run.js";
 import { categorizeTranscriptHead, classifyTranscript, estimateSessionCost, groupByProject, readTranscriptHead, } from "./pipeline/projects.js";
 import { persistProjectDecisions, promptProjectDecisions, } from "./cli/projectSelect.js";
@@ -399,8 +401,10 @@ program
                 ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`skipped ${collapseHome(p.target)}`));
                 continue;
             }
-            const ok = applyPlan(p);
-            ui.row(ok ? ui.success(ui.CHECK) : ui.errorColor(ui.CROSS), ui.text(collapseHome(p.target)));
+            const result = applyPlan(p);
+            ui.row(result.ok ? ui.success(ui.CHECK) : ui.errorColor(ui.CROSS), ui.text(result.ok || result.reason === undefined
+                ? collapseHome(p.target)
+                : `${collapseHome(p.target)} — ${result.reason}`));
         }
     }
     finally {
@@ -479,18 +483,21 @@ program
 }));
 program
     .command("lint")
-    .description("Run orphan, staleness, and contradiction checks on the vault")
+    .description("Run orphan, stray-file, staleness, and contradiction checks on the vault")
     .option("--orphans", "Run only the orphan check (free)")
+    .option("--strays", "Run only the stray-file check (free)")
     .option("--stale", "Run only the staleness check (free)")
     .option("--contradictions", "Run only the contradiction check (Haiku tokens)")
     .action(runAction(async (opts) => {
     const cfg = loadConfig();
     const db = new StateDb();
     try {
-        const runAll = !opts.orphans && !opts.stale && !opts.contradictions;
+        const runAll = !opts.orphans && !opts.strays && !opts.stale && !opts.contradictions;
         const checks = [];
         if (runAll || opts.orphans)
             checks.push("orphans");
+        if (runAll || opts.strays)
+            checks.push("strays");
         if (runAll || opts.stale)
             checks.push("stale");
         if (runAll || opts.contradictions)
@@ -498,6 +505,7 @@ program
         ui.header("lint");
         ui.blank();
         let orphanCount = 0;
+        let strayCount = 0;
         let staleCount = 0;
         let contradictionCount = 0;
         let issues = 0;
@@ -517,6 +525,27 @@ program
                 }
             }
         }
+        if (runAll || opts.strays) {
+            const sp = ui.spinner("checking stray files").start();
+            const r = strayFileCheck(cfg, db);
+            sp.stop();
+            strayCount = r.strays.length;
+            issues += strayCount;
+            if (strayCount === 0) {
+                ui.row(ui.success(ui.CHECK), `${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 (runAll || opts.stale) {
             const sp = ui.spinner("checking staleness").start();
             const stale = stalenessCheck(cfg, db);
@@ -558,6 +587,7 @@ program
                 color: issues > 0 ? ui.errorColor : ui.success,
             },
             orphans: { value: orphanCount, color: ui.muted },
+            strays: { value: strayCount, color: ui.muted },
             stale: { value: staleCount, color: ui.muted },
             contradictions: { value: contradictionCount, color: ui.muted },
         });
@@ -1208,6 +1238,14 @@ program
     .option("--project <slug>", "Filter by project")
     .option("--limit <n>", "Max notes to review in this session", "50")
     .action(runAction(runReview));
+program
+    .command("prune")
+    .description("Demote agent-derived notes to .rejected/ (dry run by default)")
+    .option("--apply", "Actually demote (default is a dry run)")
+    .option("--restore", "Restore every pruned note to its exact prior state")
+    .action(runAction(async (opts) => {
+    await pruneCommand(opts);
+}));
 program
     .command("doctor")
     .description("Run diagnostic checks on Vir installation")