Audit-hardening pass for secret and misconfiguration scanning (#977)

* fix(security): dedupe concurrent compose-stack scans

Track stack scans in scanningImages keyed stack:<nodeId>:<stackName>.
The /scan/stack route returns 409 when an in-flight scan exists, and
the service-side check is the real correctness barrier (the route
pre-check is a fast-path optimization that mirrors scanImage). The
dedup key release lives in a try/finally so failed scans free the
slot for retry.

Why: scanComposeStack had no equivalent of scanImage's scanningImages
guard, so two simultaneous calls for the same stack would both run
trivy config, both insert a vulnerability_scans row, and double-
process the result.

* feat(security): acknowledge misconfig findings

Adds a parallel acknowledgement system for Trivy misconfig findings
that mirrors cve_suppressions: a new misconfig_acknowledgements table,
read-time enrichment via the new misconfig-ack-filter utility, REST
CRUD endpoints, fleet-sync replication from control to replicas, a
Settings panel, and an Acknowledge button on the Misconfigs tab.

Schema and behavior parity with cve_suppressions:
  - UNIQUE(rule_id, COALESCE(stack_pattern, '')) so fleet-wide acks
    collide as expected
  - blockIfReplica on every write
  - Audit-log entries name the scope (rule_id, stack_pattern) but
    never the reason text
  - replicated_from_control flag controls UI delete affordance and
    drives clearReplicatedRows on demote/reanchor
  - Validators reused: validateStackPatternForRedos for glob safety,
    sanitizeForLog for log fragments

SARIF export emits an external/accepted suppression entry per
acknowledged misconfig, matching the CVE pattern.

Per-row Acknowledge dialog prefills stack_pattern with the scan's
stack_context so the default scope is "rule + this stack only" and an
operator must broaden explicitly.

Tests: misconfig-ack-filter (15) and misconfig-ack-routes (23)
including the duplicate-409 case for both pinned and fleet-wide acks.

* fix(security): reap orphaned trivy tmp dirs at startup

When the buildEnv path writes a per-scan DOCKER_CONFIG dir under
os.tmpdir() and the process crashes before the finally block runs,
the dir leaks. Mirrors GitSourceService.sweepStaleTempDirs:
exported sweepStaleTrivyTempDirs is fire-and-forget at boot,
removes prefix-matching dirs older than 1 hour, swallows
permission/race failures, logs a single line if any were reaped.

* perf(security): emit per-batch summary for scanAllNodeImages

Adds one diag() line at the end of scanAllNodeImages summarising
unique image count, scanned, skipped, failed, violation count, and
elapsed time. Per-image diag inside scanImage stays useful for
debugging individual scans; the summary gives operators a single
fleet-level checkpoint when developer_mode is on.

* perf(security): cap SARIF export at 5000 findings per type

Replace the unbounded fetchAllPages walk on /scans/:id/sarif with a
hard limit of 5000 findings per type. When any type trips the cap,
emit run-level properties.truncated=true plus row_limit and per-type
totals so downstream tooling can flag the export as partial.
Console-warns for ops visibility.

A scan with 50k vulns previously streamed every row into memory
before serialising; the cap bounds memory and serialisation time at
the cost of completeness on pathological scans.

* docs(env): document TRIVY_BIN host-binary override

The env var is honored by TrivyService.detectTrivy as a fallback when
no managed install is present, but it was undocumented in
.env.example. Adds the var with a comment explaining precedence
(managed > TRIVY_BIN > PATH).

* test(security): cover scanComposeStack failure modes

Two new cases drive the existing try/catch through real failure
paths:
  - Malformed Trivy stdout: row flips to status='failed' with the
    parser error preserved on `error`.
  - execFile rejection: row flips to status='failed' with a string
    error message.

Pairs with the existing dedup tests so the failure path now also
verifies the scan row state, not just the thrown exception.

* test(e2e): security scanner + misconfig acknowledgement flow

Seven Playwright tests covering the scanner UI and the new
acknowledgement system end-to-end:
  - Trivy availability gate (skips suite when binary absent so CI
    without Trivy can opt out via E2E_SKIP_TRIVY=1)
  - Stack config scan completes and records misconfig findings
  - Concurrent stack scan returns 409 from the dedup gate
  - Misconfig ack POST creates and lists on Settings
  - Duplicate (rule_id, stack_pattern) returns 409
  - Malformed rule_id (shell metacharacters) returns 400
  - Misconfigs tab renders against a real stack scan

Tests drive the API for behaviour assertions and the UI only for
shell-rendering checks; the visual snapshot suite owns screenshots.

* docs(features): add misconfig acknowledgement workflow and SARIF cap

Refreshes vulnerability-scanning.mdx with:
  - Misconfig acknowledgements section covering the per-row dialog,
    Settings panel, scope/matching rules, and SARIF emission
  - Tier table row for the new feature
  - SARIF section note on the 5000 row-per-type cap and the
    properties.truncated marker for partial exports
  - Troubleshooting entries: SARIF cap, hidden Acknowledge button,
    findings resurfacing after delete, Trivy DB phone-home, and
    409 on concurrent compose-stack scans

* fix(ci): clear backend lint and CodeQL alerts

- Remove the dead fetchAllPages helper in routes/security.ts. It lost
  its callers when the SARIF endpoint switched to direct paged reads
  for the truncation cap. ESLint flagged it as unused.
- Switch the trivy-tmp-cleanup test helper to fs.mkdtempSync. Building
  paths under os.tmpdir() with predictable names tripped CodeQL's
  js/insecure-temporary-file rule (high severity), which warns about
  symlink-pre-creation attacks even in test code. mkdtempSync appends
  a process-random suffix and creates the dir atomically; the
  sencho-trivy- prefix is preserved so the production sweep still
  matches the test fixtures.

backend/src/services/TrivyService.ts

@@ -26,6 +26,43 @@ const SCAN_TIMEOUT_MS = 5 * 60 * 1000;
 const SBOM_TIMEOUT_MS = 3 * 60 * 1000;
 export const DIGEST_CACHE_TTL_MS = 24 * 60 * 60 * 1000;
 
+const TRIVY_TEMP_DIR_PREFIX = 'sencho-trivy-';
+const TRIVY_TEMP_DIR_MAX_AGE_MS = 60 * 60 * 1000; // 1 hour
+
+/**
+ * Sweep leftover sencho-trivy-* temp dirs in the system tmp dir whose mtime
+ * is older than 1 hour. Runs once at service boot to clean up DOCKER_CONFIG
+ * dirs orphaned by a crashed scan process. Best-effort; swallows readdir or
+ * unlink failures so a quirky tmp dir cannot block startup.
+ */
+export async function sweepStaleTrivyTempDirs(): Promise<void> {
+    const tmp = os.tmpdir();
+    let entries: string[];
+    try {
+        entries = await fs.promises.readdir(tmp);
+    } catch {
+        return;
+    }
+    const cutoff = Date.now() - TRIVY_TEMP_DIR_MAX_AGE_MS;
+    let removed = 0;
+    for (const entry of entries) {
+        if (!entry.startsWith(TRIVY_TEMP_DIR_PREFIX)) continue;
+        const full = path.join(tmp, entry);
+        try {
+            const stat = await fs.promises.stat(full);
+            if (stat.mtimeMs < cutoff) {
+                await fs.promises.rm(full, { recursive: true, force: true });
+                removed++;
+            }
+        } catch {
+            /* race: dir already gone, or permissions; skip */
+        }
+    }
+    if (removed > 0) {
+        console.log(`[Trivy] Reaped ${removed} stale tmp dir(s) under ${tmp}`);
+    }
+}
+
 function diag(msg: string, ...args: unknown[]): void {
     if (isDebugEnabled()) console.log(`[Trivy:diag] ${sanitizeForLog(msg)}`, ...args);
 }
@@ -459,10 +496,18 @@ class TrivyService {
         return `${nodeId}:${imageRef}`;
     }
 
+    private stackScanKey(nodeId: number, stackName: string): string {
+        return `stack:${nodeId}:${stackName}`;
+    }
+
     isScanning(nodeId: number, imageRef: string): boolean {
         return this.scanningImages.has(this.scanKey(nodeId, imageRef));
     }
 
+    isScanningStack(nodeId: number, stackName: string): boolean {
+        return this.scanningImages.has(this.stackScanKey(nodeId, stackName));
+    }
+
     async scanImage(
         imageRef: string,
         nodeId: number,
@@ -835,129 +880,137 @@ class TrivyService {
         if (!(await fsvc.hasComposeFile(resolved))) {
             throw new Error(`No compose file found for stack: ${stackName}`);
         }
-
-        const db = DatabaseService.getInstance();
-        const scanId = db.createVulnerabilityScan({
-            node_id: nodeId,
-            image_ref: `stack:${stackName}`,
-            image_digest: null,
-            scanned_at: Date.now(),
-            total_vulnerabilities: 0,
-            critical_count: 0,
-            high_count: 0,
-            medium_count: 0,
-            low_count: 0,
-            unknown_count: 0,
-            fixable_count: 0,
-            secret_count: 0,
-            misconfig_count: 0,
-            scanners_used: 'config',
-            highest_severity: null,
-            os_info: null,
-            trivy_version: this.version,
-            scan_duration_ms: null,
-            triggered_by: triggeredBy,
-            status: 'in_progress',
-            error: null,
-            stack_context: stackName,
-        });
-        const startedAt = Date.now();
+        const dedupKey = this.stackScanKey(nodeId, stackName);
+        if (this.scanningImages.has(dedupKey)) {
+            throw new Error('Already scanning this stack');
+        }
+        this.scanningImages.add(dedupKey);
         try {
-            const { env, cleanup } = await this.buildEnv();
-            try {
-                const args = ['config', '--format', 'json', '--quiet', resolved];
-                const { stdout } = await execFileAsync(binary, args, {
-                    env,
-                    timeout: SCAN_TIMEOUT_MS,
-                    maxBuffer: 64 * 1024 * 1024,
-                });
-                const { misconfigs } = parseTrivyOutput(stdout);
-                let critical = 0,
-                    high = 0,
-                    medium = 0,
-                    low = 0,
-                    unknown = 0;
-                for (const m of misconfigs) {
-                    switch (m.severity) {
-                        case 'CRITICAL':
-                            critical++;
-                            break;
-                        case 'HIGH':
-                            high++;
-                            break;
-                        case 'MEDIUM':
-                            medium++;
-                            break;
-                        case 'LOW':
-                            low++;
-                            break;
-                        default:
-                            unknown++;
-                    }
-                }
-                const highestSeverity: VulnSeverity | null =
-                    critical > 0 ? 'CRITICAL'
-                        : high > 0 ? 'HIGH'
-                        : medium > 0 ? 'MEDIUM'
-                        : low > 0 ? 'LOW'
-                        : unknown > 0 ? 'UNKNOWN'
-                        : null;
-                db.updateVulnerabilityScan(scanId, {
-                    scanned_at: Date.now(),
-                    critical_count: critical,
-                    high_count: high,
-                    medium_count: medium,
-                    low_count: low,
-                    unknown_count: unknown,
-                    misconfig_count: misconfigs.length,
-                    highest_severity: highestSeverity,
-                    trivy_version: this.version,
-                    scan_duration_ms: Date.now() - startedAt,
-                    status: 'completed',
-                });
-                db.insertMisconfigFindings(
-                    scanId,
-                    misconfigs.map((m) => ({
-                        rule_id: m.ruleId,
-                        check_id: m.checkId,
-                        severity: m.severity,
-                        title: m.title,
-                        message: m.message,
-                        resolution: m.resolution,
-                        target: m.target,
-                        primary_url: m.primaryUrl,
-                    })),
-                );
-                const stored = db.getVulnerabilityScan(scanId);
-                if (!stored) throw new Error('Scan vanished after write');
-                try {
-                    const evaluation = db.evaluateScanAgainstPolicies(
-                        nodeId,
-                        stored,
-                        FleetSyncService.getSelfIdentity(),
-                    );
-                    if (evaluation) {
-                        db.setScanPolicyEvaluation(scanId, evaluation);
-                        stored.policy_evaluation = JSON.stringify(evaluation);
-                    }
-                } catch (err) {
-                    console.warn(
-                        `[Trivy] policy evaluation failed for stack scanId=${scanId}:`,
-                        getErrorMessage(err, 'unknown error'),
-                    );
-                }
-                return stored;
-            } finally {
-                cleanup();
-            }
-        } catch (error) {
-            const msg = getErrorMessage(error, 'Stack scan failed');
-            db.updateVulnerabilityScan(scanId, {
-                status: 'failed',
-                error: msg,
-                scan_duration_ms: Date.now() - startedAt,
+            const db = DatabaseService.getInstance();
+            const scanId = db.createVulnerabilityScan({
+                node_id: nodeId,
+                image_ref: `stack:${stackName}`,
+                image_digest: null,
+                scanned_at: Date.now(),
+                total_vulnerabilities: 0,
+                critical_count: 0,
+                high_count: 0,
+                medium_count: 0,
+                low_count: 0,
+                unknown_count: 0,
+                fixable_count: 0,
+                secret_count: 0,
+                misconfig_count: 0,
+                scanners_used: 'config',
+                highest_severity: null,
+                os_info: null,
+                trivy_version: this.version,
+                scan_duration_ms: null,
+                triggered_by: triggeredBy,
+                status: 'in_progress',
+                error: null,
+                stack_context: stackName,
             });
-            throw error;
+            const startedAt = Date.now();
+            try {
+                const { env, cleanup } = await this.buildEnv();
+                try {
+                    const args = ['config', '--format', 'json', '--quiet', resolved];
+                    const { stdout } = await execFileAsync(binary, args, {
+                        env,
+                        timeout: SCAN_TIMEOUT_MS,
+                        maxBuffer: 64 * 1024 * 1024,
+                    });
+                    const { misconfigs } = parseTrivyOutput(stdout);
+                    let critical = 0,
+                        high = 0,
+                        medium = 0,
+                        low = 0,
+                        unknown = 0;
+                    for (const m of misconfigs) {
+                        switch (m.severity) {
+                            case 'CRITICAL':
+                                critical++;
+                                break;
+                            case 'HIGH':
+                                high++;
+                                break;
+                            case 'MEDIUM':
+                                medium++;
+                                break;
+                            case 'LOW':
+                                low++;
+                                break;
+                            default:
+                                unknown++;
+                        }
+                    }
+                    const highestSeverity: VulnSeverity | null =
+                        critical > 0 ? 'CRITICAL'
+                            : high > 0 ? 'HIGH'
+                            : medium > 0 ? 'MEDIUM'
+                            : low > 0 ? 'LOW'
+                            : unknown > 0 ? 'UNKNOWN'
+                            : null;
+                    db.updateVulnerabilityScan(scanId, {
+                        scanned_at: Date.now(),
+                        critical_count: critical,
+                        high_count: high,
+                        medium_count: medium,
+                        low_count: low,
+                        unknown_count: unknown,
+                        misconfig_count: misconfigs.length,
+                        highest_severity: highestSeverity,
+                        trivy_version: this.version,
+                        scan_duration_ms: Date.now() - startedAt,
+                        status: 'completed',
+                    });
+                    db.insertMisconfigFindings(
+                        scanId,
+                        misconfigs.map((m) => ({
+                            rule_id: m.ruleId,
+                            check_id: m.checkId,
+                            severity: m.severity,
+                            title: m.title,
+                            message: m.message,
+                            resolution: m.resolution,
+                            target: m.target,
+                            primary_url: m.primaryUrl,
+                        })),
+                    );
+                    const stored = db.getVulnerabilityScan(scanId);
+                    if (!stored) throw new Error('Scan vanished after write');
+                    try {
+                        const evaluation = db.evaluateScanAgainstPolicies(
+                            nodeId,
+                            stored,
+                            FleetSyncService.getSelfIdentity(),
+                        );
+                        if (evaluation) {
+                            db.setScanPolicyEvaluation(scanId, evaluation);
+                            stored.policy_evaluation = JSON.stringify(evaluation);
+                        }
+                    } catch (err) {
+                        console.warn(
+                            `[Trivy] policy evaluation failed for stack scanId=${scanId}:`,
+                            getErrorMessage(err, 'unknown error'),
+                        );
+                    }
+                    return stored;
+                } finally {
+                    cleanup();
+                }
+            } catch (error) {
+                const msg = getErrorMessage(error, 'Stack scan failed');
+                db.updateVulnerabilityScan(scanId, {
+                    status: 'failed',
+                    error: msg,
+                    scan_duration_ms: Date.now() - startedAt,
+                });
+                throw error;
+            }
+        } finally {
+            this.scanningImages.delete(dedupKey);
         }
     }
 
@@ -968,6 +1021,7 @@ class TrivyService {
         if (this.source === 'none') {
             throw new Error('Trivy is not available on this host');
         }
+        const batchStartedAt = Date.now();
         const images = await DockerController.getInstance(nodeId).getImages();
         const imageRefs = new Set<string>();
         for (const img of images as Array<{ RepoTags?: string[] }>) {
@@ -1040,6 +1094,11 @@ class TrivyService {
             }
             await new Promise((r) => setTimeout(r, 300));
         }
+        diag(
+            `scanAllNodeImages: nodeId=${nodeId} unique=${imageRefs.size} `
+            + `scanned=${scanned} skipped=${skipped} failed=${failed} `
+            + `violations=${violations.length} elapsedMs=${Date.now() - batchStartedAt}`,
+        );
         return { scanned, skipped, failed, severity, violations };
     }