peaks-loop 4.0.51 → 4.0.53

package/dist/cli/commands/codegraph-commands.js

@@ -1,11 +1,27 @@
+// src/cli/commands/codegraph-commands.ts
+//
+// The codegraph verbs that MUTATE or PROXY: `repair-exclude`, `repair-index`,
+// `init`, `affected`, plus the commander registration for every codegraph
+// subcommand.
+//
+// D1 (rid 2026-09-17-oversize-and-scale, the 800-line file-size cap) moved
+// the shared invocation runtime to `codegraph-command-runtime.ts` and the
+// `status` integrity gate to `codegraph-status-command.ts`, both verbatim.
+// This path keeps its public surface: `registerCodegraphCommands` is defined
+// here and `rewriteBareCodegraphHints` / `attributeUpstreamUpToDateLine` are
+// re-exported below, so every existing importer still resolves.
 import { InvalidArgumentError } from 'commander';
 import { statSync } from 'node:fs';
 import { resolve } from 'node:path';
-import { createCodegraphInvocation, executeCodegraphInvocation, defaultCodegraphInitGuard, writeCodegraphMarker, writeCodegraphAffectedContext, CodegraphInitConflictError } from '../../services/codegraph/codegraph-service.js';
-import { CODEGRAPH_INTEGRITY_EXIT_CODE, inspectCodegraphExcludeIntegrity, isCodegraphExcludeConfigPresent, renderCodegraphExcludeIntegrityLines } from '../../services/codegraph/codegraph-exclude-integrity.js';
+import { createCodegraphInvocation, executeCodegraphInvocation, defaultCodegraphInitGuard, resolveProjectRoot, writeCodegraphMarker, writeCodegraphAffectedContext, CodegraphInitConflictError } from '../../services/codegraph/codegraph-service.js';
 import { repairCodegraphExcludeFromProject } from '../../services/codegraph/codegraph-exclude-repair.js';
 import { fail, ok } from 'peaks-loop-shared/result';
-import { getErrorMessage, printResult, redactSensitiveErrorMessage } from '../cli-helpers.js';
+import { printResult, redactSensitiveErrorMessage } from '../cli-helpers.js';
+import { printCodegraphFailure, runCodegraphCommand } from './codegraph-command-runtime.js';
+import { runCodegraphStatusCommand } from './codegraph-status-command.js';
+// Re-exported so the D1 split is invisible to importers of THIS path.
+export { rewriteBareCodegraphHints } from './codegraph-command-runtime.js';
+export { attributeUpstreamUpToDateLine } from './codegraph-status-command.js';
 function addPeaksJsonOption(command) {
     return command.option('--peaks-json', 'print Peaks error envelope as machine-readable JSON');
 }
@@ -22,219 +38,118 @@ function parsePositiveInteger(value) {
     }
     return parsed;
 }
-function printCodegraphFailure(io, command, error, asJson, exitCode = 1) {
-    printResult(io, fail(command, 'CODEGRAPH_COMMAND_FAILED', redactSensitiveErrorMessage(getErrorMessage(error)), {}, ['Check the codegraph command options and project path before retrying']), asJson);
-    process.exitCode = exitCode;
-}
-/**
- * Rewrites bare upstream `codegraph <subcommand>` hints to the peaks-loop
- * equivalent (`peaks codegraph <subcommand>`). The upstream binary is a
- * nested transitive dependency and is NOT on PATH, so an LLM that follows
- * a bare hint like `Run "codegraph init" to initialize` would hit
- * "command not found". Already-prefixed `peaks codegraph ...` hints and
- * other `codegraph` references (e.g. `@colbymchenry/codegraph`) are left
- * untouched.
- */
-export function rewriteBareCodegraphHints(text) {
-    return text.replace(/(?<![\w-])(?<!peaks\s)codegraph(?=\s+(?:status|init|index|query|files|context|affected)\b)/g, 'peaks codegraph');
-}
-const ANSI_SGR_PATTERN = /\x1b\[[0-9;]*m/g;
-/**
- * Upstream `status` answers a different question than peaks-loop's
- * integrity gate: upstream says "the on-disk graph matches the last scan"
- * (true), peaks says "that graph covers the repository" (false when rules
- * exclude tracked files). Both verdicts are correct, but an unqualified
- * `[OK] Index is up to date` printed above our `[FAIL] ...` reads as
- * "nothing to see here" — and the OK is the line the eye lands on first.
- * The exit code and the JSON envelope are already right; only this line
- * lies by juxtaposition.
- *
- * So: keep upstream's wording — the line stays recognizable, and the
- * Files/Nodes counts around it are untouched — but drop the bare OK
- * marker and name the only question it answers. Clean runs never reach
- * this, so their output stays byte-identical.
- *
- * The match is anchored to THAT line. An earlier version keyed on
- * `includes('up to date')`, which is content-blind: upstream prints other
- * `[OK] ... are up to date` lines (a language-server or watcher line is the
- * observed one), and each of those was rewritten into a claim about the
- * INDEX — a misattribution introduced by a change whose entire purpose was
- * to stop misleading output. Anything that is not the index line is passed
- * through byte-for-byte, tail note and all.
- */
-const INDEX_UP_TO_DATE_RE = /^\[OK\]\s+Index is up to date\b/i;
-export function attributeUpstreamUpToDateLine(stdout) {
-    return stdout
-        .split('\n')
-        .map((line) => {
-        const visible = line.replace(ANSI_SGR_PATTERN, '').trim();
-        if (!INDEX_UP_TO_DATE_RE.test(visible)) {
-            return line;
-        }
-        // Only the OK marker is downgraded and the attribution appended: the
-        // rest of the line — including whatever upstream wrote after it — is
-        // preserved, so nothing upstream actually said is replaced.
-        const withoutOk = visible.replace(/^\[OK\]\s*/, '');
-        return `[i] ${withoutOk} (upstream: matches the last scan only; repository coverage is answered below)`;
-    })
-        .join('\n');
-}
-async function runCodegraphCommand(io, command, options, asJson, attributeStdout) {
-    try {
-        const invocation = createCodegraphInvocation(options);
-        const result = await executeCodegraphInvocation(invocation);
-        if (result.exitCode !== null && result.exitCode !== 0 && asJson === true) {
-            printCodegraphFailure(io, command, new Error(result.stderr || result.stdout || `codegraph exited with code ${result.exitCode}`), true, result.exitCode);
-            return;
-        }
-        const didFail = result.exitCode !== null && result.exitCode !== 0;
-        const rewritten = rewriteBareCodegraphHints(result.stdout);
-        const stdout = attributeStdout === undefined ? rewritten : attributeStdout(rewritten);
-        const stderr = rewriteBareCodegraphHints(result.stderr);
-        if (stdout.length > 0) {
-            io.stdout((didFail ? redactSensitiveErrorMessage(stdout) : stdout).trimEnd());
-        }
-        if (stderr.length > 0) {
-            io.stderr((didFail ? redactSensitiveErrorMessage(stderr) : stderr).trimEnd());
-        }
-        if (didFail) {
-            process.exitCode = result.exitCode;
-        }
-    }
-    catch (error) {
-        printCodegraphFailure(io, command, error, asJson);
+// " Include now admits 7 of 9 extractor-supported tracked file(s)." — printed
+// only when the ratio reports a SHORTFALL, i.e. when the repair has left
+// files the extractor supports unadmitted. That is the one reading of this
+// sentence an operator can act on.
+//
+// What this used to say, and why it was wrong: the denominator was fed from
+// the reconciler's admitted count — the NUMERATOR's own expression — so the
+// clause could only ever print "N of N", and it was gated on
+// `after > before` with a "(was N)" trailer computed by a second full glob
+// pass. A repo with 10 supported tracked files of which 5 were admitted was
+// told "5 of 5", asserting total coverage that nothing had measured. The
+// denominator is now an independent measurement (see the report field), and
+// the trailer — whose only consumer was this sentence — is gone with the
+// pass that produced it (perf: 11.73 ms of the repair entry's +14.13 ms, on
+// every automatic seam including no-ops).
+//
+// Silence when the ratio is complete is deliberate: "2 of 2" is true but
+// says nothing, and the patterns that changed are already named by the
+// caller's own sentence.
+function admittingClause(report) {
+    if (report.trackedSourceCount === 0 || report.includeAdmittedAfter >= report.trackedSourceCount) {
+        return '';
     }
+    return ` Include now admits ${report.includeAdmittedAfter} of ${report.trackedSourceCount} extractor-supported tracked file(s).`;
 }
-/**
- * `--peaks-json` machine report for `status`. Carries the upstream
- * result AND the peaks-loop integrity verdict as one JSON document so a
- * CI job can gate on `data.integrity.gap` / `data.integrity.rulesToRemove`
- * without scraping human text.
- */
-async function runCodegraphStatusJson(io, options, integrity, integrityWarning) {
-    let result;
-    try {
-        result = await executeCodegraphInvocation(createCodegraphInvocation({ subcommand: 'status', project: options.project }));
-    }
-    catch (error) {
-        printCodegraphFailure(io, 'codegraph.status', error, true);
-        return;
-    }
-    const upstream = {
-        exitCode: result.exitCode,
-        stdout: rewriteBareCodegraphHints(result.stdout).trimEnd(),
-        stderr: redactSensitiveErrorMessage(rewriteBareCodegraphHints(result.stderr)).trimEnd()
-    };
-    const upstreamFailed = result.exitCode !== null && result.exitCode !== 0;
-    if (integrity?.gap === true) {
-        printResult(io, fail('codegraph.status', 'CODEGRAPH_INDEX_INCOMPLETE', `codegraph index is incomplete: ${integrity.excludedTrackedCount} of ${integrity.trackedSourceCount} tracked source files are excluded by ${integrity.rulesToRemove.length} rule(s).`, { upstream, integrity, integrityWarning }, ['Run `peaks codegraph repair-exclude --project <root>` to drop the offending rules and rebuild the index.']), true);
-    }
-    else if (upstreamFailed) {
-        printResult(io, fail('codegraph.status', 'CODEGRAPH_COMMAND_FAILED', redactSensitiveErrorMessage(upstream.stderr || upstream.stdout || `codegraph exited with code ${String(result.exitCode)}`), { upstream, integrity, integrityWarning }, ['Check the codegraph project path before retrying']), true);
-    }
-    else {
-        printResult(io, ok('codegraph.status', { upstream, integrity, integrityWarning }), true);
-    }
-    if (upstreamFailed) {
-        process.exitCode = result.exitCode ?? 1;
+const REPAIR_MODES = {
+    exclude: {
+        commandId: 'codegraph.repair-exclude',
+        reindex: true,
+        noopNote: 'Nothing to repair in the codegraph config; nothing was written.'
+    },
+    index: {
+        commandId: 'codegraph.repair-index',
+        // 'force' is upstream's `clear()` + full re-index — the only documented
+        // way to drop rows for files deleted in an earlier commit.
+        reindex: 'force',
+        noopNote: 'The codegraph config already admits every supported tracked file and blocks none; the index was still rebuilt from scratch.'
     }
+};
+// One sentence, the same shape in both modes, because both modes run the
+// same two-axis repair — only the rebuild differs.
+//
+// A1 (`2026-09-17-codegraph-msg-and-refresh`): EACH COUNT NAMES ITS OWN AXIS.
+// The previous wording ended one sentence about both axes with a single
+// "recovering N tracked source file(s)", fed by `filesRecovered` — the
+// EXCLUDE axis' counter. On this repo it printed "Added 5 include pattern(s)
+// and removed 0 exclude rule(s), recovering 0 tracked source file(s)." while
+// those 5 patterns had just admitted 31 tracked source files (30 `.mjs` + 1
+// `.cjs`): a true statement about the axis that did not move, read as a
+// verdict on the one that did. The `admittingClause` could not correct it
+// either — it is silent when the coverage ratio is complete, which is
+// exactly the state a fresh include repair produces.
+//
+// So: the include clause carries the include axis' own file delta and the
+// exclude clause carries the exclude axis' own count, and a reader cannot
+// attribute either number to the other clause. No combined total is printed,
+// because there is no honest single number here — the two axes recover
+// disjoint sets (one widens admission, the other unblocks admitted files)
+// and only the first of them is cheap enough to measure on every repair.
+function appliedRepairNote(report) {
+    return (`Added ${report.includePatternsAdded.length} include pattern(s), newly admitting ${report.includeFilesRecovered} tracked source file(s), and removed ${report.rulesRemoved.length} exclude rule(s), recovering ${report.filesRecovered} tracked source file(s) that a rule had been hiding.` +
+        admittingClause(report) +
+        ` Config backed up to ${report.backupPath ?? ''}.`);
 }
 /**
- * `peaks codegraph status` with an integrity gate.
- *
- * The upstream status is still proxied verbatim (that is what the
- * command has always done), but a clean upstream "index is up to date"
- * is no longer sufficient: when git-tracked source files are being
- * excluded by the config, the command says so, names the rules and
- * files, and exits non-zero.
- *
- * Read-only by construction — it imports the integrity inspector, never
- * the repair writer. Fixing the config is `peaks codegraph init`
- * (fresh) or `peaks codegraph repair-exclude` (explicit).
- */
-async function runCodegraphStatusCommand(io, options, asJson) {
-    let integrity = null;
-    let integrityWarning = null;
-    const projectRoot = resolve(options.project);
-    try {
-        // Never initialized here → no exclude list is in play, so there is
-        // nothing to report. Staying silent keeps `status` honest and
-        // unchanged for projects that do not use codegraph at all.
-        integrity = isCodegraphExcludeConfigPresent(projectRoot)
-            ? inspectCodegraphExcludeIntegrity(projectRoot)
-            : null;
-    }
-    catch (error) {
-        // Not a git work tree, no config yet, malformed config — the
-        // upstream status is still worth printing, so degrade to a warning
-        // instead of failing the whole command.
-        integrityWarning = getErrorMessage(error);
-    }
-    if (asJson === true) {
-        await runCodegraphStatusJson(io, options, integrity, integrityWarning);
-    }
-    else {
-        // Only when the gate found a gap: upstream's `[OK] Index is up to
-        // date` answers "consistent with the last scan", and printing it
-        // unqualified right above our `[FAIL]` tells the reader two opposite
-        // things at once. Clean runs get no transform and stay byte-identical.
-        await runCodegraphCommand(io, 'codegraph.status', { subcommand: 'status', project: options.project }, false, integrity?.gap === true ? attributeUpstreamUpToDateLine : undefined);
-        if (integrityWarning !== null) {
-            io.stdout(`[WARN] codegraph exclude integrity not evaluated: ${integrityWarning}`);
-        }
-        else if (integrity !== null) {
-            for (const line of renderCodegraphExcludeIntegrityLines(integrity)) {
-                io.stdout(line);
-            }
-        }
-    }
-    if (integrity?.gap === true) {
-        process.exitCode = CODEGRAPH_INTEGRITY_EXIT_CODE;
-    }
-}
-/**
- * Explicit repair path: reconcile → drop offending rules → back up the
- * config → rebuild the index. Mirrors the automatic step `init` runs
+ * Explicit repair path: reconcile both config axes → back up the config →
+ * rewrite it → rebuild the index. Mirrors the automatic step `init` runs
  * after a fresh upstream init, for workspaces that were already
  * initialized before the integrity gate existed.
  */
-async function runCodegraphRepairExcludeCommand(io, options, asJson) {
+async function runCodegraphRepairCommand(io, options, asJson, mode) {
+    const spec = REPAIR_MODES[mode];
     let projectRoot;
     try {
-        const candidate = resolve(options.project);
-        if (!statSync(candidate).isDirectory()) {
-            throw new Error('Project path must exist and be a directory');
-        }
-        projectRoot = candidate;
+        // `resolveProjectRoot`, not a hand-rolled `resolve` + `statSync`: it is
+        // the canonicalizer every codegraph invocation already goes through
+        // (`createCodegraphInvocation`), so the config path this verb reports
+        // and writes names the SAME directory the spawn and the other verbs use
+        // even when `--project` is a symlink, a short name or a differently
+        // cased alias. The error path is unchanged.
+        projectRoot = resolveProjectRoot(options.project);
     }
     catch (error) {
-        printCodegraphFailure(io, 'codegraph.repair-exclude', error, asJson);
+        printCodegraphFailure(io, spec.commandId, error, asJson);
         return;
     }
-    const report = await repairCodegraphExcludeFromProject(projectRoot);
+    const report = await repairCodegraphExcludeFromProject(projectRoot, undefined, {
+        reindex: spec.reindex
+    });
     // Where the notes go matters: `printResult` renders every `warnings`
     // entry to stderr with a `warning: ` prefix, so a confirmation parked
     // in the third slot reads as a problem — and a real warning parked
     // there double-prefixes. Confirmations go to `nextActions`; only a
     // genuine `report.warning` reaches `warnings`, verbatim.
-    const confirmations = [];
-    if (report.applied) {
-        confirmations.push(`Removed ${report.rulesRemoved.length} exclude rule(s), recovering ${report.filesRecovered} tracked source file(s). Config backed up to ${report.backupPath}.`);
-    }
-    else {
-        confirmations.push('No tracked source file is excluded by the codegraph config; nothing to repair.');
-    }
-    if (report.applied) {
+    const confirmations = [
+        report.applied ? appliedRepairNote(report) : spec.noopNote
+    ];
+    if (report.applied || mode === 'index') {
         confirmations.push('Re-run `peaks codegraph status --project <root>` to confirm the gap is closed.');
     }
-    printResult(io, ok('codegraph.repair-exclude', {
+    printResult(io, ok(spec.commandId, {
         applied: report.applied,
         rulesRemoved: report.rulesRemoved,
+        includePatternsAdded: report.includePatternsAdded,
         filesRecovered: report.filesRecovered,
+        includeFilesRecovered: report.includeFilesRecovered,
+        includeAdmittedAfter: report.includeAdmittedAfter,
         trackedSourceCount: report.trackedSourceCount,
         configPath: report.configPath,
         backupPath: report.backupPath,
         reindexed: report.reindexed,
+        forcedRebuild: report.forcedRebuild,
         warning: report.warning
     }, report.warning === null ? [] : [report.warning], confirmations), asJson);
     // A repair that could not run to completion (or could not reindex)
@@ -325,18 +240,20 @@ async function runCodegraphInitCommand(io, options, asJson) {
         catch {
             // intentionally swallowed — surface as warning below
         }
-        // Upstream `init` writes its 99-rule default `exclude` template,
-        // some of which collide with real source directories in this
-        // project. Left alone, a fresh clone / new machine gets an index
-        // that silently omits tracked source files while `status` says it
-        // is up to date. Reconcile now, drop the offending rules, and
-        // rebuild the index — a fresh init is the one moment this is both
-        // safe (nothing has been indexed yet) and necessary (`.codegraph/`
-        // is gitignored, so every clone starts from the default template).
+        // Upstream `init` writes BOTH default templates: a 99-rule `exclude`
+        // list (some rules collide with real source directories in this
+        // project) and a 32-entry `include` list (which omits five extensions
+        // upstream's own extractor supports). Left alone, a fresh clone / new
+        // machine gets an index that silently omits tracked source files while
+        // `status` says it is up to date. Reconcile now, append the missing
+        // include patterns, drop the offending rules, and rebuild the index — a
+        // fresh init is the one moment this is both safe (nothing has been
+        // indexed yet) and necessary (`.codegraph/` is gitignored, so every
+        // clone starts from the default templates).
         //
         // Never throws: a failure here is reported as a warning, not a
         // failed init (the init itself already succeeded).
-        const excludeRepair = await repairCodegraphExcludeFromProject(projectRoot);
+        const configRepair = await repairCodegraphExcludeFromProject(projectRoot);
         // These are confirmations, not warnings: `printResult` renders every
         // `warnings` entry to stderr behind a `warning: ` prefix, so a fully
         // successful init used to print a wall of `warning:` lines for what
@@ -344,9 +261,19 @@ async function runCodegraphInitCommand(io, options, asJson) {
         const initNotes = [
             `Stamped peaks-loop marker at ${guardOutcome.codegraphDir}/.peaks-loop-marker`
         ];
-        if (excludeRepair.applied) {
-            initNotes.push(`Removed ${excludeRepair.rulesRemoved.length} exclude rule(s) that blocked tracked source files, recovering ${excludeRepair.filesRecovered} file(s); config backed up to ${excludeRepair.backupPath}.`);
-            if (excludeRepair.reindexed) {
+        if (configRepair.applied) {
+            if (configRepair.includePatternsAdded.length > 0) {
+                // A1 (2026-09-17): the include axis names its OWN file delta here too.
+                // Naming the patterns alone left the same gap the repair note had —
+                // a reader learned which extensions were appended but not how many
+                // tracked files that admitted, and this note is the ONLY place a
+                // fresh `init` reports the include repair.
+                initNotes.push(`Added ${configRepair.includePatternsAdded.length} include pattern(s) upstream's extractor supports but its default template omits, newly admitting ${configRepair.includeFilesRecovered} tracked source file(s) (${configRepair.includePatternsAdded.join(', ')}).${admittingClause(configRepair)}`);
+            }
+            if (configRepair.rulesRemoved.length > 0) {
+                initNotes.push(`Removed ${configRepair.rulesRemoved.length} exclude rule(s) that blocked tracked source files, recovering ${configRepair.filesRecovered} file(s); config backed up to ${configRepair.backupPath ?? ''}.`);
+            }
+            if (configRepair.reindexed) {
                 initNotes.push('Rebuilt the codegraph index over the recovered files.');
             }
         }
@@ -355,17 +282,21 @@ async function runCodegraphInitCommand(io, options, asJson) {
             codegraphDir: guardOutcome.codegraphDir,
             markerWritten: true,
             excludeRepair: {
-                applied: excludeRepair.applied,
-                rulesRemoved: excludeRepair.rulesRemoved,
-                filesRecovered: excludeRepair.filesRecovered,
-                reindexed: excludeRepair.reindexed,
-                backupPath: excludeRepair.backupPath,
-                warning: excludeRepair.warning
+                applied: configRepair.applied,
+                rulesRemoved: configRepair.rulesRemoved,
+                includePatternsAdded: configRepair.includePatternsAdded,
+                filesRecovered: configRepair.filesRecovered,
+                includeFilesRecovered: configRepair.includeFilesRecovered,
+                includeAdmittedAfter: configRepair.includeAdmittedAfter,
+                trackedSourceCount: configRepair.trackedSourceCount,
+                reindexed: configRepair.reindexed,
+                backupPath: configRepair.backupPath,
+                warning: configRepair.warning
             }
         }, 
         // Verbatim: `printResult` supplies the `warning: ` prefix, so a
         // prefix added here would render as `warning: warning: ...`.
-        excludeRepair.warning === null ? [] : [excludeRepair.warning], initNotes), asJson);
+        configRepair.warning === null ? [] : [configRepair.warning], initNotes), asJson);
     }
     catch (error) {
         printCodegraphFailure(io, 'codegraph.init', error, asJson);
@@ -442,41 +373,55 @@ export function registerCodegraphCommands(program, io) {
     addProjectOption(codegraph.command('status').description('Show codegraph status, including the exclude integrity gate')).action((options) => runCodegraphStatusCommand(io, options, options.peaksJson));
     addProjectOption(codegraph
         .command('repair-exclude')
-        .description('Drop codegraph exclude rules that block tracked source files, then rebuild the index')).action((options) => runCodegraphRepairExcludeCommand(io, options, options.peaksJson));
+        .description('Normalize the codegraph include list, drop exclude rules that block tracked source files, then rebuild the index')).action((options) => runCodegraphRepairCommand(io, options, options.peaksJson, 'exclude'));
+    addProjectOption(codegraph
+        .command('repair-index')
+        .description('Repair both codegraph config axes, then rebuild the index from scratch (drops rows for deleted files)')).action((options) => runCodegraphRepairCommand(io, options, options.peaksJson, 'index'));
     addProjectOption(codegraph.command('init').description('Initialize codegraph for a project')).action((options) => runCodegraphInitCommand(io, options, options.peaksJson));
     addProjectOption(codegraph
         .command('index')
         .description('Index a project with codegraph')
         .option('--force', 'force reindexing')
-        .option('--quiet', 'reduce upstream output')).action((options) => runCodegraphCommand(io, 'codegraph.index', {
-        subcommand: 'index',
-        project: options.project,
-        ...(options.force === true ? { force: true } : {}),
-        ...(options.quiet === true ? { quiet: true } : {})
-    }, options.peaksJson));
+        .option('--quiet', 'reduce upstream output')).action(async (options) => {
+        // `runCodegraphCommand` returns "upstream failed" for the one caller
+        // that ranks exit-code precedence (`status`); every other command just
+        // awaits it, so it is discarded here rather than leaked to commander.
+        await runCodegraphCommand(io, 'codegraph.index', {
+            subcommand: 'index',
+            project: options.project,
+            ...(options.force === true ? { force: true } : {}),
+            ...(options.quiet === true ? { quiet: true } : {})
+        }, options.peaksJson);
+    });
     addProjectOption(codegraph
         .command('query')
         .description('Query codegraph')
         .argument('<search>', 'search text')
         .option('--json', 'forward JSON output flag to upstream codegraph')
-        .option('--limit <n>', 'maximum result count', parsePositiveInteger)).action((search, options) => runCodegraphCommand(io, 'codegraph.query', {
-        subcommand: 'query',
-        project: options.project,
-        search,
-        ...(options.json === true ? { json: true } : {}),
-        ...(options.limit !== undefined ? { limit: options.limit } : {})
-    }, options.peaksJson));
+        .option('--limit <n>', 'maximum result count', parsePositiveInteger)).action(async (search, options) => {
+        await runCodegraphCommand(io, 'codegraph.query', {
+            subcommand: 'query',
+            project: options.project,
+            search,
+            ...(options.json === true ? { json: true } : {}),
+            ...(options.limit !== undefined ? { limit: options.limit } : {})
+        }, options.peaksJson);
+    });
     addProjectOption(codegraph
         .command('files')
         .description('List codegraph files')
         .option('--json', 'forward JSON output flag to upstream codegraph')
-        .option('--max-depth <n>', 'maximum traversal depth', parsePositiveInteger)).action((options) => runCodegraphCommand(io, 'codegraph.files', {
-        subcommand: 'files',
-        project: options.project,
-        ...(options.json === true ? { json: true } : {}),
-        ...(options.maxDepth !== undefined ? { maxDepth: options.maxDepth } : {})
-    }, options.peaksJson));
-    addProjectOption(codegraph.command('context').description('Build task context with codegraph').argument('<task>', 'task text')).action((task, options) => runCodegraphCommand(io, 'codegraph.context', { subcommand: 'context', project: options.project, task }, options.peaksJson));
+        .option('--max-depth <n>', 'maximum traversal depth', parsePositiveInteger)).action(async (options) => {
+        await runCodegraphCommand(io, 'codegraph.files', {
+            subcommand: 'files',
+            project: options.project,
+            ...(options.json === true ? { json: true } : {}),
+            ...(options.maxDepth !== undefined ? { maxDepth: options.maxDepth } : {})
+        }, options.peaksJson);
+    });
+    addProjectOption(codegraph.command('context').description('Build task context with codegraph').argument('<task>', 'task text')).action(async (task, options) => {
+        await runCodegraphCommand(io, 'codegraph.context', { subcommand: 'context', project: options.project, task }, options.peaksJson);
+    });
     addProjectOption(codegraph
         .command('affected')
         .description('Find code affected by files')

package/dist/cli/commands/codegraph-status-command.d.ts

@@ -0,0 +1,22 @@
+import { type ProgramIO } from '../cli-helpers.js';
+import { type CommonCodegraphOptions } from './codegraph-command-runtime.js';
+export declare function attributeUpstreamUpToDateLine(stdout: string): string;
+/**
+ * `peaks codegraph status` with an integrity gate.
+ *
+ * The upstream status is still proxied verbatim (that is what the
+ * command has always done), but a clean upstream "index is up to date"
+ * is no longer sufficient: when git-tracked source files are being
+ * excluded by the config, or the index itself does not cover the
+ * repository, the command says so and names the rules and files.
+ *
+ * SEVERITY (user decision, option C): the exclude gate keeps its shipped
+ * blocking behaviour (exit 74); the index gate is ADVISORY by default and
+ * blocking only when `PEAKS_CODEGRAPH_INDEX_STRICT` is set. A detected
+ * gap is the finding either way — only the tag and the exit code move.
+ *
+ * Read-only by construction — it imports the integrity inspectors, never
+ * the repair writer. Fixing the config is `peaks codegraph init`
+ * (fresh) or `peaks codegraph repair-exclude` (explicit).
+ */
+export declare function runCodegraphStatusCommand(io: ProgramIO, options: CommonCodegraphOptions, asJson?: boolean): Promise<void>;