@herbertgao/pi-extensions 2026.8.6 → 2026.8.7

package/node_modules/pi-lens/dist/clients/runtime-session.js

@@ -1,10 +1,14 @@
 import * as nodeFs from "node:fs";
 import * as path from "node:path";
+import { resetBoundedTelemetry } from "./bounded-telemetry.js";
 import { createDeadline, yieldIfOverBudget } from "./cooperative-budget.js";
 import { deadCodeIssueCount } from "./dead-code-client.js";
 import { logDeadCodeScan } from "./dead-code-logger.js";
-import { resetDegradationLedger } from "./degradation-ledger.js";
+import { incrementDegradationCount, resetDegradationLedger, } from "./degradation-ledger.js";
 import { getDiagnosticTracker } from "./diagnostic-tracker.js";
+import { resetPsScriptAnalyzerAvailability } from "./dispatch/runners/psscriptanalyzer.js";
+import { resetInstallRetryLatches } from "./dispatch/runners/utils/availability-policy.js";
+import { resetLazyInstallAttempts } from "./dispatch/runners/utils/lazy-installer.js";
 import { resetDispatchAvailabilityState } from "./dispatch/runners/utils/runner-helpers.js";
 import { clearAllSessions as clearFileTimeSessions } from "./file-time.js";
 import { getGlobalPiLensDir, getKnipIgnorePatterns, getProjectDataDir, } from "./file-utils.js";
@@ -16,11 +20,17 @@ import { detectProjectLanguageProfile, getDefaultStartupTools, } from "./languag
 import { logLatency } from "./latency-logger.js";
 import { runLogCleanup } from "./log-cleanup.js";
 import { initLSPConfig, loadLSPConfig } from "./lsp/config.js";
+import { resetWorkspaceDiagnosticsCacheSession } from "./lsp/workspace-diagnostics-session.js";
+import { resetDirectLspCommandAvailability } from "./lsp/server.js";
 import { loadLspService } from "./lsp-lazy.js";
+import { resetManagedToolRefreshSession } from "./installer/managed-tool-refresh-session.js";
+import { resetResolvedPathCache } from "./installer/index.js";
+import { _resetPackageManagerCache } from "./package-manager.js";
+import { clearFormatterCache } from "./formatters.js";
 import { isAtOrAboveHomeDir } from "./path-utils.js";
 import { isPrintMode } from "./print-mode.js";
 import { readLatestProjectSequence, readLatestProjectSequenceAsync, } from "./project-changes.js";
-import { getProjectSnapshotPath, hydrateRuntimeFromProjectSnapshot, isProjectSnapshotFresh, isProjectSnapshotMetaStale, loadProjectSnapshot, PROJECT_SNAPSHOT_VERSION, readProjectSnapshotMeta, saveRuntimeProjectSnapshot, } from "./project-snapshot.js";
+import { getProjectSnapshotPath, getProjectSnapshotLegacyPath, hydrateRuntimeFromProjectSnapshot, hydrateRuntimeFromProjectSnapshotIfIdle, isProjectSnapshotFresh, isProjectSnapshotMetaStale, loadProjectSnapshot, loadProjectSnapshotExportsAndRules, PROJECT_SNAPSHOT_VERSION, readProjectSnapshotMeta, saveRuntimeProjectSnapshot, } from "./project-snapshot.js";
 import { clearTsconfigPathsCache } from "./review-graph/tsconfig-paths.js";
 import { scanProjectRules } from "./rules-scanner.js";
 import { resetSafeSpawnWindowsCommandCache } from "./safe-spawn.js";
@@ -33,6 +43,27 @@ import { isWarmAttached } from "./warm-attach.js";
 import { setSessionLanguages } from "./widget-state.js";
 import { logWordIndex } from "./word-index-logger.js";
 import { resetWorkspaceTopology } from "./workspace-topology.js";
+import { resetZizmorTokenAvailability } from "./zizmor-config.js";
+const HOST_STALL_THRESHOLD_MS = 30_000;
+function logHostReadyDelay(deps, cwd) {
+    if (!deps.emitHostReadyDelay ||
+        deps.sessionStartMonotonicAt === undefined ||
+        deps.extensionLoadedAt === undefined) {
+        return;
+    }
+    const durationMs = Math.max(0, deps.sessionStartMonotonicAt - deps.extensionLoadedAt);
+    logLatency({
+        type: "phase",
+        filePath: cwd,
+        phase: "host_ready_delay",
+        durationMs,
+        metadata: {
+            hostStallSuspected: durationMs > HOST_STALL_THRESHOLD_MS,
+            sessionStart: "first-process-session",
+            reason: deps.sessionReason,
+        },
+    });
+}
 function resolveSnapshotRoot(cwd) {
     const resolvedCwd = path.resolve(cwd);
     const nearest = findNearestProjectRoot(resolvedCwd);
@@ -79,6 +110,91 @@ function snapshotSequenceBase(root) {
         sinceSeq: meta.seq,
     };
 }
+/**
+ * #1785: one bounded ledger record per timed-out sequence read, so a real
+ * occurrence is diagnosable from the ledger alone rather than only from a
+ * `dbg` line that most hosts never surface. Carries the project root and the
+ * on-disk snapshot's age/size (when one exists) — the identity AC1 asks for:
+ * which project, how stale/large the snapshot that got skipped was.
+ */
+function recordSnapshotSequenceTimeout(args) {
+    let reason = "sequence read timed out; no snapshot on disk";
+    try {
+        const stat = nodeFs.statSync(args.snapshotPath);
+        reason = `sequence read timed out; snapshot age=${Math.round(Date.now() - stat.mtimeMs)}ms size=${stat.size}b`;
+    }
+    catch {
+        // No snapshot on disk yet — the reason above already covers it.
+    }
+    incrementDegradationCount({
+        kind: "snapshot-sequence-read-timeout",
+        subject: args.snapshotRoot,
+        reason,
+    });
+}
+/**
+ * #1785: the synchronous freshness check made a conservative call with the
+ * `UNKNOWN_PROJECT_SEQ` sentinel (never hydrate when the real sequence is
+ * unknown). Once the deferred read resolves — a deterministic completion
+ * signal, not a sleep — this re-checks freshness against the now-known
+ * sequence and hydrates late when the snapshot really was current, instead of
+ * leaving the runtime without `cachedExports`/`projectRulesScan` for the rest
+ * of the session.
+ *
+ * #1785 review round F5 (design (a), replacing rounds 1-3's synchronous
+ * capture entirely): quick mode's own cold-start warmup ALREADY loads the
+ * on-disk snapshot for its own purposes — `cachedSnapshot` at the top of the
+ * warmup body, used to reuse a still-fresh `startupScan` verdict — strictly
+ * BEFORE the warmup's own possible save (`saveRuntimeProjectSnapshot`, only
+ * reached when that verdict was NOT fresh). Reusing THAT already-loaded
+ * value costs nothing new: the read was always going to happen regardless of
+ * this fix, and it is guaranteed to predate any overwrite the SAME warmup
+ * invocation might go on to make — a read-before-write invariant of the
+ * warmup's own code, not something this function has to defend against with
+ * a race window of its own. `getWarmupOwnSnapshotRead` is a closure over a
+ * per-`handleSessionStart`-call LOCAL variable (never module-scope — #1785
+ * F6 is exactly the class of bug a module-scope holder here would
+ * reintroduce) that the warmup publishes into once its own read completes.
+ *
+ * When the getter still returns `undefined` — the deferred read resolved
+ * before the warmup got that far (or no warmup was ever armed by this call:
+ * a later quick-mode call in the same process, print mode, full mode) —
+ * there is nothing published yet, so this falls back to a live re-load via
+ * `loadProjectSnapshotExportsAndRules`. That fallback is exactly as safe as
+ * the primary path: if the warmup hasn't reached its own read yet, it
+ * certainly hasn't saved yet either (same invariant), so disk still holds
+ * whatever was there before any warmup activity.
+ *
+ * Both the published value and the fallback re-load are the narrow,
+ * postings-free `ProjectSnapshotExportsAndRules` shape — never the full
+ * `loadProjectSnapshot`. This path only ever hydrates
+ * `cachedExports`/`projectRulesScan`; it can NOT hydrate `wordIndex` even
+ * when the underlying snapshot would otherwise have one, because the narrow
+ * type never carries it. That is intentional, not a regression: F2's hazard
+ * was this exact path nulling a `wordIndex` that quick mode's warmup had, in
+ * the meantime, built for real — the warmup remains the sole source of a
+ * late-arriving `wordIndex` for the interactive path.
+ */
+function retroactivelyHydrateAfterDeferredSequence(args) {
+    return (latestSeq) => {
+        const published = args.getWarmupOwnSnapshotRead();
+        const snapshot = published !== undefined
+            ? published
+            : loadProjectSnapshotExportsAndRules(args.snapshotRoot);
+        if (!snapshot ||
+            snapshot.version !== PROJECT_SNAPSHOT_VERSION ||
+            snapshot.seq !== latestSeq.projectSeq) {
+            return;
+        }
+        const hydrated = hydrateRuntimeFromProjectSnapshotIfIdle(args.runtime, snapshot);
+        if (hydrated) {
+            args.dbg(`session_start: deferred sequence read confirmed snapshot freshness — hydrating cachedExports/projectRulesScan late (seq=${snapshot.seq})`);
+        }
+        else {
+            args.dbg(`session_start: deferred sequence read confirmed snapshot freshness (seq=${snapshot.seq}), but the runtime already has live state (warmup or another task got there first) — skipping late hydration to avoid clobbering it`);
+        }
+    };
+}
 function loadSnapshotBodyUnlessStale(args) {
     const meta = readProjectSnapshotMeta(args.root);
     if (meta && isProjectSnapshotMetaStale(meta, args.currentProjectSeq)) {
@@ -90,12 +206,17 @@ function loadSnapshotBodyUnlessStale(args) {
         skippedStale: false,
     };
 }
-function describeSnapshotMiss(snapshot, currentProjectSeq) {
+function describeSnapshotMiss(snapshot, currentProjectSeq, args) {
+    if (args.skippedStale)
+        return "stale-meta-gate";
     if (!snapshot)
-        return "missing";
+        return args.bodyPresent ? "invalid-body" : "missing";
     if (snapshot.seq !== currentProjectSeq) {
         return `stale(seq=${snapshot.seq}, current=${currentProjectSeq})`;
     }
+    // Defensive-only arm: parseSnapshot rejects incompatible versions, and a
+    // same-sequence parsed snapshot is fresh. Keep this classification explicit
+    // so a future loader change cannot collapse it into a generic miss.
     return "incompatible";
 }
 function logProjectSnapshotProbe(args) {
@@ -104,7 +225,7 @@ function logProjectSnapshotProbe(args) {
         args.dbg(`project_snapshot: loaded seq=${args.snapshot.seq} exports=${args.snapshot.cachedExports.length} files=${Object.keys(args.snapshot.files ?? {}).length} reverseDeps=${Object.keys(args.snapshot.reverseDeps ?? {}).length} startupScan=${Boolean(args.snapshot.startupScan)} languageProfile=${Boolean(args.snapshot.languageProfile)}`);
     }
     else {
-        args.dbg(`project_snapshot: miss reason=${describeSnapshotMiss(args.snapshot, args.currentProjectSeq)}`);
+        args.dbg(`project_snapshot: miss reason=${args.missReason}`);
     }
 }
 function resolveStartupMode() {
@@ -171,7 +292,7 @@ const UNKNOWN_PROJECT_SEQ = -1;
  * logs its own `session_start_sequence_read_deferred_reseed` phase.
  */
 async function readSequenceWithBudget(args) {
-    const { snapshotRoot, base, cwd, runtime, sessionGeneration, dbg } = args;
+    const { snapshotRoot, base, cwd, runtime, sessionGeneration, dbg, onDeferredSequenceResolved, } = args;
     const readPromise = readLatestProjectSequenceAsync(snapshotRoot, base);
     let timeoutHandle;
     const timeoutPromise = new Promise((resolve) => {
@@ -224,6 +345,7 @@ async function readSequenceWithBudget(args) {
                 metadata: { entries: latestSeq.fileSeqByPath.size, deferred: true },
             });
             dbg(`session_start: deferred sequence read completed — reseeded projectSeq=${latestSeq.projectSeq} fileSeqEntries=${latestSeq.fileSeqByPath.size}`);
+            onDeferredSequenceResolved?.(latestSeq);
         })
             .catch((err) => {
             dbg(`session_start: deferred sequence read failed: ${err}`);
@@ -375,6 +497,47 @@ function firePreinstallDefaults(ensureTool, dbg, startupDefaults) {
         });
     }
 }
+/**
+ * Default delay before the managed-tool version refresh runs (#1730). Long
+ * enough that `session_start`, the startup scans, and the tool preinstalls have
+ * all settled — the refresh may spawn one `npm update`, and that must never
+ * compete with the work the user is waiting on.
+ */
+const MANAGED_TOOL_REFRESH_DELAY_MS = 30_000;
+/**
+ * Schedule the periodic managed-tool refresh (#1730) on an unref'd background
+ * timer.
+ *
+ * `session_start`'s own cost here is a single `setTimeout` registration: the
+ * refresh module is not even imported until the timer fires. The timer is
+ * unref'd so a one-shot process exits without waiting for it, matching the
+ * warmup timer above. Whether a refresh actually runs is decided inside
+ * `runManagedToolRefresh` against a PERSISTED per-tool stamp, so a launch loop
+ * cannot escalate the weekly cadence.
+ */
+function scheduleManagedToolRefresh(dbg) {
+    const delayMs = Number(process.env.PI_LENS_TOOL_REFRESH_DELAY_MS ?? MANAGED_TOOL_REFRESH_DELAY_MS);
+    const timer = setTimeout(() => {
+        void (async () => {
+            try {
+                const refresh = await import("./installer/managed-tool-refresh.js");
+                const outcome = await refresh.runManagedToolRefresh();
+                if (outcome.skipped) {
+                    dbg(`session_start tool-refresh: skipped (${outcome.skipped})`);
+                    return;
+                }
+                for (const result of outcome.refreshed) {
+                    dbg(`session_start tool-refresh: ${result.toolId} ${result.ok ? "ok" : "failed"}` +
+                        `${result.changed ? ` ${result.previousVersion ?? "unknown"} → ${result.currentVersion}` : " (unchanged)"}`);
+                }
+            }
+            catch (err) {
+                dbg(`session_start tool-refresh: error ${err}`);
+            }
+        })();
+    }, Number.isFinite(delayMs) ? delayMs : MANAGED_TOOL_REFRESH_DELAY_MS);
+    timer.unref?.();
+}
 async function probePrettierInstall(ensureTool, dbg, analysisRoot) {
     const pkgPath = path.join(analysisRoot, "package.json");
     try {
@@ -715,7 +878,7 @@ function scheduleStartupScans(deps, runtime, sessionGeneration, analysisRoot, sn
             // KnipClient skips before probing/installing when analysisRoot is not a real
             // JS/Knip project. This avoids running knip from Unity/C#/generic repos.
             const startMs = Date.now();
-            const knipResult = await knipClient.analyze(analysisRoot, getKnipIgnorePatterns());
+            const knipResult = await knipClient.analyze(analysisRoot, getKnipIgnorePatterns(), { projectSeq: runtime.projectSeq });
             if (!runtime.isCurrentSession(sessionGeneration))
                 return;
             if (knipResult.success) {
@@ -1121,6 +1284,12 @@ export const SESSION_START_GUIDANCE = [
 ];
 export async function handleSessionStart(deps) {
     resetDegradationLedger();
+    // #1743: the bounded-telemetry per-turn counters. The rising-edge state is
+    // NOT here — it is the ledger's own tally, reset on the line above. These
+    // counters are keyed by turn index, and a new session restarts turn
+    // numbering at 0, so without this a stale count could survive a session
+    // boundary that happened to land on the same index.
+    resetBoundedTelemetry();
     const handlerEnteredAt = Date.now();
     const sessionStartMs = deps.sessionStartFiredAt ?? handlerEnteredAt;
     const cwdForTelemetry = deps.ctxCwd ?? process.cwd();
@@ -1175,6 +1344,11 @@ export async function handleSessionStart(deps) {
     //   (an explicit env var still takes highest precedence).
     // Tunable: PI_LENS_WARMUP_DELAY_MS adjusts the warmup delay.
     let startupMode = resolveStartupMode();
+    // SAFETY: these two flags are process-lifetime state pi-lens stashes on
+    // `globalThis` so a second extension instance in the same process sees the
+    // first one's warmup. There is no ambient declaration for them, and adding
+    // one would let any module write them. Both are declared OPTIONAL here, so
+    // the reads below are `undefined`-safe on a process where nothing set them.
     const processGlobals = globalThis;
     const isFirstSessionOfProcess = !processGlobals.__piLensFirstSessionDone;
     if (isFirstSessionOfProcess &&
@@ -1185,6 +1359,20 @@ export async function handleSessionStart(deps) {
         startupMode = deps.startupModeOverride ?? "quick";
     }
     processGlobals.__piLensFirstSessionDone = true;
+    // #1785 F5 (round 4, design (a)): the warmup timer body below ALREADY
+    // loads the on-disk snapshot for its own purposes (`cachedSnapshot`,
+    // reused for the `startupScan` verdict cache) strictly BEFORE any save it
+    // might go on to make. This LOCAL variable — per-`handleSessionStart`-call,
+    // deliberately NOT module-scope (see #1785 F6) — lets the warmup publish
+    // that already-loaded read (narrowed to exports+rules, never the full
+    // object with `wordIndex`) for `retroactivelyHydrateAfterDeferredSequence`
+    // to reuse at zero additional cost, instead of this call paying for its
+    // own separate synchronous capture (rounds 1-3's approach, reverted here:
+    // see that function's doc comment for the full history). `undefined`
+    // means the warmup hasn't reached its own read yet (or was never armed by
+    // this call at all) — the quick-mode block's retroactive-hydration
+    // callback then falls back to a live re-load instead.
+    let warmupOwnSnapshotRead;
     // #1154: quick mode is entered on BOTH `pi -p`/`--print` (a one-shot that
     // exits right after this turn) and an interactive process's first
     // session_start (forced quick to protect keystroke latency, then warms
@@ -1232,6 +1420,23 @@ export async function handleSessionStart(deps) {
                     // reuse it instead of re-walking a possibly huge tree from
                     // scratch on every single startup.
                     const cachedSnapshot = loadProjectSnapshot(warmupSnapshotRoot);
+                    // #1785 F5 (round 4): publish this ALREADY-loaded read — narrowed
+                    // to exports+rules, never a reference to `cachedSnapshot` itself
+                    // (which carries `wordIndex`/`files`/`symbols`/`reverseDeps`) — for
+                    // `retroactivelyHydrateAfterDeferredSequence` to reuse. This read
+                    // strictly precedes the warmup's own possible save a few lines
+                    // below, so it is guaranteed to reflect disk as it stood before
+                    // THIS warmup could have touched it. Zero marginal cost: this read
+                    // already happens unconditionally for the `startupScan` verdict
+                    // cache below, with or without this fix.
+                    warmupOwnSnapshotRead = cachedSnapshot
+                        ? {
+                            version: cachedSnapshot.version,
+                            seq: cachedSnapshot.seq,
+                            cachedExports: cachedSnapshot.cachedExports,
+                            projectRulesScan: cachedSnapshot.projectRulesScan,
+                        }
+                        : null;
                     const cachedVerdict = cachedSnapshot?.startupScan;
                     let scan;
                     if (cachedVerdict &&
@@ -1381,7 +1586,7 @@ export async function handleSessionStart(deps) {
     }
     const allowBootstrapTasks = startupMode === "full";
     const quickMode = startupMode === "quick";
-    const { ctxCwd, getFlag, notify, dbg, log, runtime, metricsClient, cacheManager, testRunnerClient, goClient, rustClient, ensureTool, cleanStaleTsBuildInfo, resetDispatchBaselines, resetLSPService, } = deps;
+    const { ctxCwd, getFlag, notify, dbg, log, runtime, metricsClient, knipClient, cacheManager, testRunnerClient, goClient, rustClient, ensureTool, cleanStaleTsBuildInfo, resetDispatchBaselines, resetLSPService, } = deps;
     // Lightweight phase timer — resets after each call so each log line shows
     // the cost of that phase alone, not cumulative time from session start.
     let _phaseT = Date.now();
@@ -1415,9 +1620,66 @@ export async function handleSessionStart(deps) {
     // the tool for the rest of the process lifetime. Clear it here, same
     // boundary as the other per-session caches on this line.
     resetDispatchAvailabilityState();
+    // #1895: formatter PATH verdicts are session-scoped, but they live in
+    // formatters.ts and are not covered by the dispatch generation. Re-arm them
+    // here so a formatter installed or removed between sessions is observed by
+    // the next session. `clearFormatterCache` drops the per-cwd selection cache
+    // as well as the which latches, which is what a real re-probe needs: the
+    // selection cache answers a same-cwd lookup before any probe runs, so
+    // clearing the latches alone would leave the stale verdict standing in the
+    // one directory the user is working in.
+    clearFormatterCache();
+    // #1535: same #1266 pattern, one caller earlier — the `gh auth token` latch
+    // zizmor's spawn reads is process-lived storage whose durability contract is
+    // per SESSION, not per process. Without this, a user who runs `gh auth
+    // login` and starts a fresh session still reads the previous session's
+    // stale "no token" verdict until the cooldown (if any) happens to expire.
+    resetZizmorTokenAvailability();
+    // psscriptanalyzer's three latches (interpreter, module, -File exec) are
+    // module-local, so the generation counter above does not reach them
+    // (#1490, #1540).
+    resetPsScriptAnalyzerAvailability();
+    // #1497: the install-class retry ceiling is terminal for a SESSION, but the
+    // latches holding it live on process-lived client instances (bootstrap builds
+    // them once). Same #1266/#1490/#1535 shape — without this line "terminal for
+    // the session" is terminal for the process, and a repaired network never
+    // re-earns its `go install`.
+    resetInstallRetryLatches();
+    // #1537: the lazy-install seam's hold (`gem install rubocop`, `rustup
+    // component add`) is durable for a SESSION. Its map is module-local, so the
+    // generation counter above does not reach it — same #1490/#1497 shape. It
+    // belongs on THIS line and not on the turn_end path: the first cut cleared it
+    // from `clearFormatterRuntimeState()`, which runs every turn, so a failing
+    // install re-spawned every turn instead of once per session.
+    resetLazyInstallAttempts();
+    // #1897: direct-LSP negative availability and bare installer paths are
+    // session facts. A command or PATH entry can appear between sessions.
+    resetDirectLspCommandAvailability();
+    resetResolvedPathCache();
+    // #1653: pnpm/yarn/bun/npm's availability latches (package-manager.ts) are
+    // module-local, same #1490/#1535 shape as the two lines above — the
+    // generation counter above does not reach them. Without this line, a
+    // pnpm/yarn/bun install done mid-day stayed invisible: a genuine "missing"
+    // verdict from one session latched into the next until a process restart.
+    _resetPackageManagerCache();
+    // #1730: the managed-tool refresh budget is a per-SESSION allowance (at most
+    // one `npm update` per session). Left process-lived, one long-running pi
+    // would refresh a single tool at launch and never look at the other 21
+    // again — the same latch shape as the two lines above. The weekly cadence
+    // itself is NOT reset here: it lives in the persisted per-tool stamp, so
+    // re-arming the budget only restores the session's right to ask.
+    resetManagedToolRefreshSession();
     // #1123 item 3: a fresh session can re-report smells that a prior session
     // already surfaced once (see `checkSmellsAndNoteOnce`'s once-per-session gate).
     resetSmellsSessionState();
+    // #1782: re-arm the workspace-diagnostics cache session clock. Entries
+    // written before this instant assert findings from a session that is over,
+    // so they must revalidate before they can be served as current again.
+    resetWorkspaceDiagnosticsCacheSession(sessionStartMs);
+    // Some embedders inject a capability-shaped Knip client rather than the
+    // concrete KnipClient. Session reset is an optional lifecycle capability;
+    // its absence must not make session_start fail.
+    knipClient.resetSessionState?.();
     runtime.resetForSession(sessionStartMs);
     logLatency({
         type: "phase",
@@ -1471,11 +1733,21 @@ export async function handleSessionStart(deps) {
     // project data roots and machine-global registry root once per session start;
     // this is fire-and-forget and bounded so it never delays startup.
     const projectDataDir = getProjectDataDir(cwd);
+    // #1609 review F1: sweepOwnStagingFiles does not recurse, so the installer's
+    // bin/ and tools/ subdirectories (clients/installer/index.ts's
+    // GITHUB_BIN_DIR / TOOLS_DIR, now atomic-write.js writers too) need their
+    // own entries — otherwise an orphaned staging file from a kill mid-install
+    // (this PR's own motivating scenario) never gets reaped, and unique
+    // pid-thread-seq staging names mean repeated kills ACCUMULATE full-size
+    // orphan binaries instead of being cleaned up.
+    const globalDir = getGlobalPiLensDir();
     void sweepAtomicWriteStages([
         projectDataDir,
         path.join(projectDataDir, "cache"),
         path.join(projectDataDir, "sessions"),
-        getGlobalPiLensDir(),
+        globalDir,
+        path.join(globalDir, "bin"),
+        path.join(globalDir, "tools"),
     ]).catch(() => {
         // best-effort lifecycle cleanup — never fail session_start
     });
@@ -1483,6 +1755,12 @@ export async function handleSessionStart(deps) {
         runtime.projectRoot = cwd;
         const sequenceReadStartedAt = Date.now();
         const snapshotRoot = resolveSnapshotRoot(cwd);
+        // #1785 F5 (round 4): the getter closes over `warmupOwnSnapshotRead`
+        // directly (a `let` in this same `handleSessionStart` invocation's
+        // scope), so it reads whatever value is current AT DEFERRED-RESOLVE
+        // TIME — not whatever it was at this wiring instant. See
+        // `retroactivelyHydrateAfterDeferredSequence`'s doc comment for the
+        // full design.
         const { latestSeq, timedOut } = await readSequenceWithBudget({
             snapshotRoot,
             base: snapshotSequenceBase(snapshotRoot),
@@ -1490,6 +1768,12 @@ export async function handleSessionStart(deps) {
             runtime,
             sessionGeneration: runtime.sessionGeneration,
             dbg,
+            onDeferredSequenceResolved: retroactivelyHydrateAfterDeferredSequence({
+                getWarmupOwnSnapshotRead: () => warmupOwnSnapshotRead,
+                snapshotRoot,
+                runtime,
+                dbg,
+            }),
         });
         logLatency({
             type: "phase",
@@ -1499,6 +1783,12 @@ export async function handleSessionStart(deps) {
             durationMs: Date.now() - sequenceReadStartedAt,
             metadata: { entries: latestSeq.fileSeqByPath.size, timedOut },
         });
+        if (timedOut) {
+            recordSnapshotSequenceTimeout({
+                snapshotRoot,
+                snapshotPath: getProjectSnapshotPath(snapshotRoot),
+            });
+        }
         runtime.seedProjectSequence?.(latestSeq.projectSeq, latestSeq.fileSeqByPath);
         const effectiveSeq = runtime.projectSeq ?? latestSeq.projectSeq;
         dbg(`session_start sequence: projectSeq=${effectiveSeq} fileSeqEntries=${latestSeq.fileSeqByPath.size}`);
@@ -1522,6 +1812,8 @@ export async function handleSessionStart(deps) {
         catch {
             // Missing snapshots are the normal cold-start case.
         }
+        const snapshotBodyPresent = nodeFs.existsSync(snapshotPath) ||
+            nodeFs.existsSync(getProjectSnapshotLegacyPath(snapshotRoot));
         const snapshotGate = loadSnapshotBodyUnlessStale({
             root: snapshotRoot,
             currentProjectSeq: freshnessSeq,
@@ -1529,6 +1821,10 @@ export async function handleSessionStart(deps) {
         });
         const snapshot = snapshotGate.snapshot;
         const snapshotFresh = isProjectSnapshotFresh(snapshot, freshnessSeq);
+        const snapshotMissReason = describeSnapshotMiss(snapshot, freshnessSeq, {
+            skippedStale: snapshotGate.skippedStale,
+            bodyPresent: snapshotBodyPresent,
+        });
         logLatency({
             type: "phase",
             phase: "session_start_snapshot_load",
@@ -1539,6 +1835,7 @@ export async function handleSessionStart(deps) {
                 bytes: snapshotBytes,
                 fresh: snapshotFresh,
                 seq: snapshot?.seq ?? null,
+                reason: snapshotFresh ? undefined : snapshotMissReason,
                 ...(snapshotGate.skippedStale ? { skippedStale: true } : {}),
                 ...(timedOut ? { sequenceUnknown: true } : {}),
             },
@@ -1548,6 +1845,7 @@ export async function handleSessionStart(deps) {
             root: snapshotRoot,
             currentProjectSeq: freshnessSeq,
             snapshot,
+            missReason: snapshotMissReason,
         });
         if (snapshotFresh) {
             hydrateRuntimeFromProjectSnapshot(runtime, snapshot);
@@ -1569,6 +1867,7 @@ export async function handleSessionStart(deps) {
             durationMs: totalDurationMs,
             metadata: { mode: startupMode, reason: deps.sessionReason },
         });
+        logHostReadyDelay(deps, cwd);
         emitSmellsSessionStartLine(dbg, sessionStartMs);
         return;
     }
@@ -1605,6 +1904,20 @@ export async function handleSessionStart(deps) {
         durationMs: Date.now() - sequenceReadStartedAt,
         metadata: { entries: latestSeq.fileSeqByPath.size, timedOut },
     });
+    if (timedOut) {
+        // #1785: instrumentation only here, deliberately no
+        // `onDeferredSequenceResolved` — unlike quick mode's cold path (which
+        // does nothing when the snapshot isn't trusted), full mode's cold path
+        // actively kicks off a real rescan below to rebuild this same state.
+        // Retroactively hydrating from the on-disk snapshot once the deferred
+        // read lands could overwrite that fresher, actively-computed state with
+        // the stale disk copy — a regression, not a fix. See the PR body for the
+        // full reasoning.
+        recordSnapshotSequenceTimeout({
+            snapshotRoot,
+            snapshotPath: getProjectSnapshotPath(snapshotRoot),
+        });
+    }
     runtime.seedProjectSequence?.(latestSeq.projectSeq, latestSeq.fileSeqByPath);
     const effectiveSeq = runtime.projectSeq ?? latestSeq.projectSeq;
     dbg(`session_start sequence: projectSeq=${effectiveSeq} fileSeqEntries=${latestSeq.fileSeqByPath.size}`);
@@ -1624,6 +1937,8 @@ export async function handleSessionStart(deps) {
     catch {
         // Missing snapshots are the normal cold-start case.
     }
+    const snapshotBodyPresent = nodeFs.existsSync(snapshotPath) ||
+        nodeFs.existsSync(getProjectSnapshotLegacyPath(snapshotRoot));
     const snapshotGate = loadSnapshotBodyUnlessStale({
         root: snapshotRoot,
         currentProjectSeq: freshnessSeq,
@@ -1631,6 +1946,10 @@ export async function handleSessionStart(deps) {
     });
     const snapshot = snapshotGate.snapshot;
     const snapshotFresh = isProjectSnapshotFresh(snapshot, freshnessSeq);
+    const snapshotMissReason = describeSnapshotMiss(snapshot, freshnessSeq, {
+        skippedStale: snapshotGate.skippedStale,
+        bodyPresent: snapshotBodyPresent,
+    });
     logLatency({
         type: "phase",
         phase: "session_start_snapshot_load",
@@ -1641,6 +1960,7 @@ export async function handleSessionStart(deps) {
             bytes: snapshotBytes,
             fresh: snapshotFresh,
             seq: snapshot?.seq ?? null,
+            reason: snapshotFresh ? undefined : snapshotMissReason,
             ...(snapshotGate.skippedStale ? { skippedStale: true } : {}),
             ...(timedOut ? { sequenceUnknown: true } : {}),
         },
@@ -1650,6 +1970,7 @@ export async function handleSessionStart(deps) {
         root: snapshotRoot,
         currentProjectSeq: freshnessSeq,
         snapshot,
+        missReason: snapshotMissReason,
     });
     const freshSnapshot = snapshotFresh ? snapshot : null;
     if (freshSnapshot) {
@@ -1777,6 +2098,7 @@ export async function handleSessionStart(deps) {
     const jstsHeavyScansWillRun = startupScansWillRun && canRunStartupHeavyScans(languageProfile, "jsts");
     if (allowBootstrapTasks) {
         scheduleDeferredToolProbes(deps, languageProfile, startupDefaults, jstsHeavyScansWillRun, dbg);
+        scheduleManagedToolRefresh(dbg);
     }
     if (allowBootstrapTasks) {
         // Fire-and-forget like other tool probes
@@ -1889,6 +2211,7 @@ export async function handleSessionStart(deps) {
         durationMs: totalDurationMs,
         metadata: { mode: startupMode, reason: deps.sessionReason },
     });
+    logHostReadyDelay(deps, cwd);
     emitSmellsSessionStartLine(dbg, sessionStartMs);
 }
 /**