gsd-pi 2.76.0-dev.4100bd590 → 2.76.0-dev.479ad0e78

package/dist/resources/extensions/gsd/auto/session.js

@@ -65,6 +65,8 @@ export class AutoSession {
     currentDispatchedModelId = null;
     originalModelId = null;
     originalModelProvider = null;
+    autoModeStartThinkingLevel = null;
+    originalThinkingLevel = null;
     lastBudgetAlertLevel = 0;
     // ── Recovery ─────────────────────────────────────────────────────────────
     pendingCrashRecovery = null;
@@ -77,6 +79,17 @@ export class AutoSession {
     lastStateRebuildAt = 0;
     // ── Sidecar queue ─────────────────────────────────────────────────────
     sidecarQueue = [];
+    // ── Pre-exec gate failure context (#4551) ───────────────────────────
+    /**
+     * Persisted when a pre-execution gate fails on a plan-slice or refine-slice
+     * unit. The planning → plan-slice dispatch rule reads this field and injects
+     * the failure details into the next re-dispatch prompt so the LLM can fix the
+     * specific issues instead of producing an identical plan.
+     *
+     * Cleared after it has been consumed (injected into the prompt) to avoid
+     * stale context bleeding into unrelated slices.
+     */
+    lastPreExecFailure = null;
     // ── Tool invocation errors (#2883) ──────────────────────────────────
     /** Set when a GSD tool execution ends with isError due to malformed/truncated
      *  JSON arguments. Checked by postUnitPreVerification to break retry loops. */
@@ -137,7 +150,12 @@ export class AutoSession {
         this.unitLifetimeDispatches.clear();
     }
     get lockBasePath() {
-        return this.originalBasePath || this.basePath;
+        // Prefer originalBasePath (project root); fall back to basePath.
+        // Strip /.gsd/worktrees/ suffix if basePath is itself a worktree path
+        // to avoid reading/writing the lock inside the worktree (#3729).
+        const resolved = this.originalBasePath || this.basePath;
+        const markerIdx = resolved.indexOf("/.gsd/worktrees/");
+        return markerIdx !== -1 ? resolved.slice(0, markerIdx) : resolved;
     }
     reset() {
         this.clearTimers();
@@ -177,6 +195,8 @@ export class AutoSession {
         this.currentDispatchedModelId = null;
         this.originalModelId = null;
         this.originalModelProvider = null;
+        this.autoModeStartThinkingLevel = null;
+        this.originalThinkingLevel = null;
         this.lastBudgetAlertLevel = 0;
         // Recovery
         this.pendingCrashRecovery = null;
@@ -195,6 +215,7 @@ export class AutoSession {
         this.sidecarQueue = [];
         this.rewriteAttemptCount = 0;
         this.consecutiveCompleteBootstraps = 0;
+        this.lastPreExecFailure = null;
         this.lastToolInvocationError = null;
         this.lastGitActionFailure = null;
         this.lastGitActionStatus = null;

package/dist/resources/extensions/gsd/auto-dispatch.js

@@ -451,18 +451,31 @@ export const DISPATCH_RULES = [
     },
     {
         name: "planning → plan-slice",
-        match: async ({ state, mid, midTitle, basePath, sessionContextWindow, modelRegistry }) => {
+        match: async ({ state, mid, midTitle, basePath, sessionContextWindow, modelRegistry, session }) => {
             if (state.phase !== "planning")
                 return null;
             if (!state.activeSlice)
                 return missingSliceStop(mid, state.phase);
             const sid = state.activeSlice.id;
             const sTitle = state.activeSlice.title;
+            // #4551: Consume any persisted pre-exec failure for this slice so the
+            // re-dispatched prompt includes the exact blocked references. Clear the
+            // field immediately after reading to prevent stale context leaking into
+            // a later, unrelated plan-slice run.
+            const unitId = `${mid}/${sid}`;
+            let priorPreExecFailure;
+            if (session?.lastPreExecFailure?.unitId === unitId) {
+                priorPreExecFailure = {
+                    blockingFindings: session.lastPreExecFailure.blockingFindings,
+                    verdictExcerpt: session.lastPreExecFailure.verdictExcerpt,
+                };
+                session.lastPreExecFailure = null;
+            }
             return {
                 action: "dispatch",
                 unitType: "plan-slice",
-                unitId: `${mid}/${sid}`,
-                prompt: await buildPlanSlicePrompt(mid, midTitle, sid, sTitle, basePath, undefined, { sessionContextWindow, modelRegistry }),
+                unitId,
+                prompt: await buildPlanSlicePrompt(mid, midTitle, sid, sTitle, basePath, undefined, { sessionContextWindow, modelRegistry, priorPreExecFailure }),
             };
         },
     },

package/dist/resources/extensions/gsd/auto-model-selection.js

@@ -13,6 +13,11 @@ import { logWarning } from "./workflow-logger.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { applyModelPolicyFilter } from "./uok/model-policy.js";
 import { isModelBlocked } from "./blocked-models.js";
+function reapplyThinkingLevel(pi, level) {
+    if (!level)
+        return;
+    pi.setThinkingLevel(level);
+}
 export function resolvePreferredModelConfig(unitType, autoModeStartModel, isAutoMode = true) {
     const explicitConfig = resolveModelWithFallbacksForUnit(unitType);
     if (explicitConfig) {
@@ -58,7 +63,9 @@ export async function selectAndApplyModel(ctx, pi, unitType, unitId, basePath, p
  *  Dynamic routing only applies in auto-mode where cost optimization is expected. (#3962) */
 isAutoMode = true, 
 /** Explicit /gsd model pin captured at bootstrap for long-running auto loops. */
-sessionModelOverride) {
+sessionModelOverride, 
+/** Thinking level captured at auto-mode start and re-applied after model swaps. */
+autoModeStartThinkingLevel) {
     const uokFlags = resolveUokFlags(prefs);
     const effectiveSessionModelOverride = sessionModelOverride === undefined
         ? getSessionModelOverride(ctx.sessionManager.getSessionId())
@@ -280,10 +287,11 @@ sessionModelOverride) {
             const ok = await pi.setModel(model, { persist: false });
             if (ok) {
                 appliedModel = model;
+                reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
                 // ADR-005: Adjust active tool set for the selected model's provider capabilities.
                 // Hard-filter incompatible tools, then let extensions override via adjust_tool_set hook.
                 const activeToolNames = pi.getActiveTools();
-                const { toolNames: compatibleTools, removedTools } = adjustToolSet(activeToolNames, model.api);
+                const { toolNames: compatibleTools, removedTools } = adjustToolSet(activeToolNames, model.api, model.provider);
                 let finalToolNames = compatibleTools;
                 // Fire adjust_tool_set hook — extensions can override the filtered tool set
                 if (routingConfig.hooks !== false) {
@@ -346,12 +354,15 @@ sessionModelOverride) {
                     const byId = availableModels.find(m => m.id === autoModeStartModel.id && !isModelBlocked(basePath, m.provider, m.id));
                     if (byId) {
                         const fallbackOk = await pi.setModel(byId, { persist: false });
-                        if (fallbackOk)
+                        if (fallbackOk) {
                             appliedModel = byId;
+                            reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
+                        }
                     }
                 }
                 else {
                     appliedModel = startModel;
+                    reapplyThinkingLevel(pi, autoModeStartThinkingLevel);
                 }
             }
         }

package/dist/resources/extensions/gsd/auto-post-unit.js

@@ -30,7 +30,7 @@ import { checkPostUnitHooks, isRetryPending, consumeRetryTrigger, persistHookSta
 import { hasPendingCaptures, loadPendingCaptures, revertExecutorResolvedCaptures } from "./captures.js";
 import { debugLog } from "./debug-logger.js";
 import { runSafely } from "./auto-utils.js";
-import { getEvidence } from "./safety/evidence-collector.js";
+import { getEvidence, clearEvidenceFromDisk } from "./safety/evidence-collector.js";
 import { validateFileChanges } from "./safety/file-change-validator.js";
 // crossReferenceEvidence available for future use when verification_evidence is stored in DB
 // import { crossReferenceEvidence, type ClaimedEvidence } from "./safety/evidence-cross-ref.js";
@@ -535,7 +535,7 @@ export async function postUnitPreVerification(pctx, opts) {
                         if (taskRow) {
                             const expectedOutput = taskRow.expected_output ?? [];
                             const plannedFiles = taskRow.files ?? [];
-                            const audit = validateFileChanges(s.basePath, expectedOutput, plannedFiles);
+                            const audit = validateFileChanges(s.basePath, expectedOutput, plannedFiles, safetyConfig.file_change_allowlist);
                             if (audit && audit.violations.length > 0) {
                                 const warnings = audit.violations.filter(v => v.severity === "warning");
                                 for (const v of warnings) {
@@ -588,6 +588,16 @@ export async function postUnitPreVerification(pctx, opts) {
                         debugLog("postUnit", { phase: "safety-content-validation", error: String(e) });
                     }
                 }
+                // Clear persisted evidence file now that post-unit processing is complete
+                // (Bug #4385 — prevents stale evidence from affecting retries of same unit ID).
+                if (safetyConfig.evidence_collection && s.currentUnit.type === "execute-task" && sMid && sSid && sTid) {
+                    try {
+                        clearEvidenceFromDisk(s.basePath, sMid, sSid, sTid);
+                    }
+                    catch (e) {
+                        debugLog("postUnit", { phase: "safety-evidence-clear", error: String(e) });
+                    }
+                }
             }
         }
         catch (e) {
@@ -950,12 +960,25 @@ export async function postUnitPostVerification(pctx) {
                     const suffix = blockingChecks.length > 3 ? `\n  \u2022 ...and ${blockingChecks.length - 3} more` : "";
                     const evidenceNote = `\nSee ${sid}-PRE-EXEC-VERIFY.json for full details.`;
                     ctx.ui.notify(`Pre-execution checks failed: ${blockingCount} blocking issue${blockingCount === 1 ? "" : "s"} found\n${details}${suffix}${evidenceNote}`, "error");
+                    // Persist failure context so the next plan-slice re-dispatch can inject
+                    // it into the prompt and break the infinite loop (#4551).
+                    s.lastPreExecFailure = {
+                        unitId: currentUnit.id,
+                        blockingFindings: blockingChecks.map(c => `[${c.category}] ${c.target}: ${c.message}`),
+                        verdictExcerpt: `status=${result.status}; ${blockingCount} blocking issue${blockingCount === 1 ? "" : "s"} detected`,
+                    };
                     preExecPauseNeeded = true;
                 }
                 else if (result.status === "warn") {
                     ctx.ui.notify(`Pre-execution checks passed with warnings`, "warning");
                     // Strict mode: treat warnings as blocking
                     if (prefs?.enhanced_verification_strict === true) {
+                        const warnChecks = result.checks.filter(c => !c.passed);
+                        s.lastPreExecFailure = {
+                            unitId: currentUnit.id,
+                            blockingFindings: warnChecks.map(c => `[${c.category}] ${c.target}: ${c.message}`),
+                            verdictExcerpt: `status=${result.status} (strict mode); ${warnChecks.length} warning${warnChecks.length === 1 ? "" : "s"} treated as blocking`,
+                        };
                         preExecPauseNeeded = true;
                     }
                 }

package/dist/resources/extensions/gsd/auto-prompts.js

@@ -1223,6 +1223,20 @@ export async function buildPlanSlicePrompt(mid, _midTitle, sid, sTitle, base, le
         prependBlocks.push(`## Prior Sketch Scope (soft hint — non-binding)\n\n${options.softScopeHint.trim()}\n\n` +
             `This scope was captured during an earlier progressive-planning pass that was later disabled. Treat it as context only — you may plan beyond it if the work genuinely requires more scope. Do NOT treat this as a hard boundary.`);
     }
+    // #4551: inject pre-exec failure context so the re-dispatched plan-slice
+    // addresses the exact blocked references rather than reproducing the same plan.
+    if (options?.priorPreExecFailure) {
+        const { blockingFindings, verdictExcerpt } = options.priorPreExecFailure;
+        const findingsList = blockingFindings.length > 0
+            ? blockingFindings.map(f => `- ${f}`).join("\n")
+            : "- (no specific findings recorded)";
+        prependBlocks.push(`## Fix these specific issues from the prior pre-exec check\n\n` +
+            `The previous plan-slice attempt was blocked by pre-execution validation.\n` +
+            `Gate verdict: ${verdictExcerpt}\n\n` +
+            `Blocked references that must be resolved in this plan:\n${findingsList}\n\n` +
+            `Revise the plan so that every reference listed above is satisfied before execution begins. ` +
+            `Do not reproduce the same file paths, package names, or task ordering that caused these failures.`);
+    }
     return renderSlicePrompt({
         mid, sid, sTitle, base,
         level: level ?? resolveInlineLevel(),

package/dist/resources/extensions/gsd/auto-recovery.js

@@ -11,7 +11,7 @@ import { appendEvent } from "./workflow-events.js";
 import { atomicWriteSync } from "./atomic-write.js";
 import { clearParseCache } from "./files.js";
 import { parseRoadmap as parseLegacyRoadmap, parsePlan as parseLegacyPlan } from "./parsers-legacy.js";
-import { isDbAvailable, getTask, getSlice, getSliceTasks, getPendingGates, updateTaskStatus, updateSliceStatus } from "./gsd-db.js";
+import { isDbAvailable, getTask, getSlice, getSliceTasks, getPendingGates, updateTaskStatus, updateSliceStatus, insertSlice } from "./gsd-db.js";
 import { isValidationTerminal } from "./state.js";
 import { getErrorMessage } from "./error-utils.js";
 import { logWarning, logError } from "./workflow-logger.js";
@@ -220,12 +220,25 @@ export function verifyExpectedArtifact(unitType, unitId, base) {
     // RESEARCH file. Without this, resolveExpectedArtifactPath returns null and
     // the retry/escalation machinery silently re-dispatches forever.
     //
+    // #4068: Also treat a PARALLEL-BLOCKER placeholder as a terminal completion
+    // so that timeout-recovery can write the blocker, have verifyExpectedArtifact
+    // return true, and let the dispatch loop advance past this unit.  Without
+    // this, the blocker is written but verification still returns false, the unit
+    // is never cleared from unitDispatchCount, and on the next iteration the
+    // dispatch rule (which correctly skips parallel-research when PARALLEL-BLOCKER
+    // exists) returns null — leaving the loop stuck re-deriving indefinitely.
+    //
     // NOTE: this predicate mirrors the dispatch rule at
     // auto-dispatch.ts parallel-research-slices — keep the two in sync.
     if (unitType === "research-slice" && unitId.endsWith("/parallel-research")) {
         const { milestone: mid } = parseUnitId(unitId);
         if (!mid)
             return false;
+        // #4068: PARALLEL-BLOCKER written by timeout-recovery is a terminal state.
+        const blockerPath = resolveExpectedArtifactPath(unitType, unitId, base);
+        if (blockerPath && existsSync(blockerPath)) {
+            return true;
+        }
         const roadmapFile = resolveMilestoneFile(base, mid, "ROADMAP");
         if (!roadmapFile || !existsSync(roadmapFile)) {
             logWarning("recovery", `verify-fail ${unitType} ${unitId}: roadmap missing`);
@@ -497,6 +510,24 @@ export function writeBlockerPlaceholder(unitType, unitId, base, reason) {
                 logWarning("recovery", `appendEvent failed for slice recovery: ${e instanceof Error ? e.message : String(e)}`);
             }
         }
+        // Insert a placeholder complete slice so deriveState sees activeMilestoneSlices.length > 0
+        // and exits the pre-planning phase. Without this, activeMilestoneSlices stays empty
+        // after the blocker ROADMAP.md is written, causing deriveState to return phase:'pre-planning'
+        // indefinitely and re-dispatching plan-milestone in an infinite loop (#4378).
+        if (unitType === "plan-milestone" && mid) {
+            try {
+                insertSlice({ id: "S00-blocker", milestoneId: mid, title: "Blocker placeholder — planning failed", status: "complete", sequence: 0 });
+            }
+            catch (e) {
+                logWarning("recovery", `insertSlice placeholder failed for plan-milestone recovery: ${e instanceof Error ? e.message : String(e)}`);
+            }
+            try {
+                appendEvent(base, { cmd: "plan-milestone", params: { milestoneId: mid }, ts, actor: "system", trigger_reason: "blocker-placeholder-recovery" });
+            }
+            catch (e) {
+                logWarning("recovery", `appendEvent failed for plan-milestone recovery: ${e instanceof Error ? e.message : String(e)}`);
+            }
+        }
     }
     return diagnoseExpectedArtifact(unitType, unitId, base);
 }

package/dist/resources/extensions/gsd/auto-start.js

@@ -30,8 +30,7 @@ import { initRoutingHistory } from "./routing-history.js";
 import { restoreHookState, resetHookState } from "./post-unit-hooks.js";
 import { resetProactiveHealing, setLevelChangeCallback } from "./doctor-proactive.js";
 import { snapshotSkills } from "./skill-discovery.js";
-import { isDbAvailable, getMilestone, openDatabase } from "./gsd-db.js";
-import { hideFooter } from "./auto-dashboard.js";
+import { isDbAvailable, getMilestone, openDatabase, getDbStatus } from "./gsd-db.js";
 import { debugLog, enableDebug, isDebugEnabled, getDebugLogPath, } from "./debug-logger.js";
 import { logWarning, logError } from "./workflow-logger.js";
 import { existsSync, mkdirSync, readdirSync, rmSync, statSync, unlinkSync, } from "node:fs";
@@ -190,8 +189,8 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
     //
     // Precedence:
     // 1) Explicit session override via /gsd model (this session)
-    // 2) GSD model preferences from PREFERENCES.md (validated against live auth)
-    // 3) Current session model from settings/session restore (if provider ready)
+    // 2) Current session model from settings/session restore (if provider ready)
+    // 3) GSD model preferences from PREFERENCES.md (validated against live auth)
     //
     // This preserves #3517 defaults while honoring explicit runtime model
     // selection for subsequent /gsd runs in the same session.
@@ -224,11 +223,14 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         }
     }
     const sessionModelReady = ctx.model && ctx.modelRegistry.isProviderRequestReady(ctx.model.provider);
+    const currentSessionModel = (sessionModelReady && ctx.model)
+        ? { provider: ctx.model.provider, id: ctx.model.id }
+        : null;
+    const startThinkingSnapshot = pi.getThinkingLevel();
     const startModelSnapshot = manualSessionOverride
+        ?? currentSessionModel
         ?? validatedPreferredModel
-        ?? (sessionModelReady && ctx.model
-            ? { provider: ctx.model.provider, id: ctx.model.id }
-            : null);
+        ?? null;
     try {
         // Validate GSD_PROJECT_ID early so the user gets immediate feedback
         const customProjectId = process.env.GSD_PROJECT_ID;
@@ -244,7 +246,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // the parent git root). See #2393 and related issue.
         const hasLocalGit = existsSync(join(base, ".git"));
         if (!hasLocalGit || isInheritedRepo(base)) {
-            const mainBranch = loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
+            const mainBranch = loadEffectiveGSDPreferences(base)?.preferences?.git?.main_branch || "main";
             nativeInit(base, mainBranch);
         }
         // Migrate legacy in-project .gsd/ to external state directory.
@@ -260,7 +262,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // Ensure .gitignore has baseline patterns.
         // ensureGitignore checks for git-tracked .gsd/ files and skips the
         // ".gsd" pattern if the project intentionally tracks .gsd/ in git.
-        const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
+        const gitPrefs = loadEffectiveGSDPreferences(base)?.preferences?.git;
         const manageGitignore = gitPrefs?.manage_gitignore;
         ensureGitignore(base, { manageGitignore });
         if (manageGitignore !== false)
@@ -286,7 +288,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             prepareWorkflowMcpForProject(ctx, base);
         }
         // Initialize GitServiceImpl
-        s.gitService = new GitServiceImpl(s.basePath, loadEffectiveGSDPreferences()?.preferences?.git ?? {});
+        s.gitService = new GitServiceImpl(s.basePath, loadEffectiveGSDPreferences(base)?.preferences?.git ?? {});
         // ── Debug mode ──
         if (!isDebugEnabled() && process.env.GSD_DEBUG === "1") {
             enableDebug(base);
@@ -319,7 +321,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // was lost due to session ending between completion and teardown.
         // Must run after DB open and before worktree entry.
         try {
-            const auditResult = auditOrphanedMilestoneBranches(base, getIsolationMode());
+            const auditResult = auditOrphanedMilestoneBranches(base, getIsolationMode(base));
             for (const msg of auditResult.recovered) {
                 ctx.ui.notify(`Orphan audit: ${msg}`, "info");
             }
@@ -337,7 +339,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         let state = await deriveState(base);
         // Stale worktree state recovery (#654)
         if (state.activeMilestone &&
-            shouldUseWorktreeIsolation() &&
+            shouldUseWorktreeIsolation(base) &&
             !detectWorktreeName(base)) {
             const wtPath = getAutoWorktreePath(base, state.activeMilestone.id);
             if (wtPath) {
@@ -352,7 +354,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         let hasSurvivorBranch = false;
         if (state.activeMilestone &&
             (state.phase === "pre-planning" || state.phase === "complete") &&
-            getIsolationMode() !== "none" &&
+            getIsolationMode(base) !== "none" &&
             !detectWorktreeName(base) &&
             !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)) {
             const milestoneBranch = `milestone/${state.activeMilestone.id}`;
@@ -413,29 +415,15 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
                 }
                 const { showSmartEntry } = await import("./guided-flow.js");
                 await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
-                invalidateAllCaches();
-                const postState = await deriveState(base);
-                if (postState.activeMilestone &&
-                    postState.phase !== "complete" &&
-                    postState.phase !== "pre-planning") {
-                    s.consecutiveCompleteBootstraps = 0; // Successfully advanced past "complete"
-                    state = postState;
-                }
-                else if (postState.activeMilestone &&
-                    postState.phase === "pre-planning") {
-                    const contextFile = resolveMilestoneFile(base, postState.activeMilestone.id, "CONTEXT");
-                    const hasContext = !!(contextFile && (await loadFile(contextFile)));
-                    if (hasContext) {
-                        state = postState;
-                    }
-                    else {
-                        ctx.ui.notify("Discussion completed but no milestone context was written. Run /gsd to try the discussion again, or /gsd auto after creating the milestone manually.", "warning");
-                        return releaseLockAndReturn();
-                    }
-                }
-                else {
-                    return releaseLockAndReturn();
-                }
+                // showSmartEntry dispatches via pi.sendMessage() which is fire-and-forget:
+                // it queues the message and returns immediately, before the LLM turn runs.
+                // Checking postState here would always see the pre-dispatch state, causing
+                // the premature "Discussion completed but..." warning (#3420).
+                //
+                // checkAutoStartAfterDiscuss (in guided-flow.ts) already handles re-entering
+                // auto-mode by calling startAutoDetached after the discussion completes.
+                // Release the lock and let the async dispatch proceed.
+                return releaseLockAndReturn();
             }
             // Active milestone exists but has no roadmap
             if (state.phase === "pre-planning") {
@@ -445,15 +433,16 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
                 if (!hasContext) {
                     const { showSmartEntry } = await import("./guided-flow.js");
                     await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
-                    invalidateAllCaches();
-                    const postState = await deriveState(base);
-                    if (postState.activeMilestone && postState.phase !== "pre-planning") {
-                        state = postState;
-                    }
-                    else {
-                        ctx.ui.notify("Discussion completed but milestone context is still missing. Run /gsd to try again.", "warning");
-                        return releaseLockAndReturn();
-                    }
+                    // showSmartEntry dispatches via pi.sendMessage() which is fire-and-forget:
+                    // it queues the message and returns immediately, before the LLM turn runs.
+                    // Checking postState here fires before the LLM has had a turn, so the
+                    // pre-planning phase would still appear unchanged and a premature warning
+                    // would be emitted (#3420).
+                    //
+                    // checkAutoStartAfterDiscuss (in guided-flow.ts) already handles re-entering
+                    // auto-mode by calling startAutoDetached after the discussion completes.
+                    // Release the lock and let the async dispatch proceed.
+                    return releaseLockAndReturn();
                 }
             }
             // Active milestone has CONTEXT-DRAFT but no full context — needs discussion
@@ -506,13 +495,14 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         s.pendingQuickTasks = [];
         s.currentUnit = null;
         s.currentMilestoneId = state.activeMilestone?.id ?? null;
-        s.originalModelId = ctx.model?.id ?? null;
-        s.originalModelProvider = ctx.model?.provider ?? null;
+        s.originalModelId = startModelSnapshot?.id ?? ctx.model?.id ?? null;
+        s.originalModelProvider = startModelSnapshot?.provider ?? ctx.model?.provider ?? null;
+        s.originalThinkingLevel = startThinkingSnapshot ?? null;
         // Register SIGTERM handler
         registerSigtermHandler(base);
         // Capture integration branch
         if (s.currentMilestoneId) {
-            if (getIsolationMode() !== "none") {
+            if (getIsolationMode(base) !== "none") {
                 captureIntegrationBranch(base, s.currentMilestoneId);
             }
             setActiveMilestoneId(base, s.currentMilestoneId);
@@ -520,7 +510,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // Guard against stale milestone branch when isolation:none (#3613).
         // A prior session with isolation:branch/worktree may have left HEAD on
         // milestone/<MID>. Auto-checkout back to the integration branch.
-        if (getIsolationMode() === "none" && nativeIsRepo(base)) {
+        if (getIsolationMode(base) === "none" && nativeIsRepo(base)) {
             try {
                 const currentBranch = nativeGetCurrentBranch(base);
                 if (currentBranch.startsWith("milestone/")) {
@@ -548,7 +538,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             return symlinkRe.test(p);
         };
         if (s.currentMilestoneId &&
-            getIsolationMode() !== "none" &&
+            getIsolationMode(base) !== "none" &&
             !detectWorktreeName(base) &&
             !isUnderGsdWorktrees(base)) {
             buildResolver().enterMilestone(s.currentMilestoneId, {
@@ -593,8 +583,21 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // call returns "db_unavailable", triggering artifact-retry which
         // re-dispatches the same task — producing an infinite loop (#2419).
         if (existsSync(gsdDbPath) && !isDbAvailable()) {
-            ctx.ui.notify("SQLite database exists but failed to open. Auto-mode cannot proceed without a working database provider. " +
-                "Check for corrupt gsd.db or missing native SQLite bindings.", "error");
+            const dbStatus = getDbStatus();
+            const phaseHint = dbStatus.lastPhase === "open"
+                ? "The database file could not be opened"
+                : dbStatus.lastPhase === "initSchema"
+                    ? "The database schema could not be initialized"
+                    : dbStatus.lastPhase === "vacuum-recovery"
+                        ? "Corruption recovery (VACUUM) failed"
+                        : dbStatus.attempted
+                            ? "The database could not be opened (phase unknown)"
+                            : "The database provider could not be loaded";
+            const errorDetail = dbStatus.lastError ? ` (${dbStatus.lastError.message})` : "";
+            const providerHint = dbStatus.provider
+                ? ` Provider: ${dbStatus.provider}.`
+                : " No SQLite provider available — check Node >= 22 or install better-sqlite3.";
+            ctx.ui.notify(`SQLite database exists but failed to open: ${gsdDbPath}. ${phaseHint}${errorDetail}.${providerHint}`, "error");
             return releaseLockAndReturn();
         }
         // Initialize metrics
@@ -608,6 +611,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
                 id: startModelSnapshot.id,
             };
         }
+        s.autoModeStartThinkingLevel = startThinkingSnapshot ?? null;
         s.manualSessionModelOverride = manualSessionOverride ?? null;
         // Apply worker model override from parallel orchestrator (#worker-model).
         // GSD_WORKER_MODEL is injected by the coordinator when parallel.worker_model
@@ -628,13 +632,10 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             }
         }
         // Snapshot installed skills
-        if (resolveSkillDiscoveryMode() !== "off") {
+        if (resolveSkillDiscoveryMode(base) !== "off") {
             snapshotSkills();
         }
         ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
-        ctx.ui.setFooter(hideFooter);
-        // Hide gsd-health during AUTO — gsd-progress is the single source of truth
-        // for last-commit / cost / health signal while auto is running.
         ctx.ui.setWidget("gsd-health", undefined);
         const modeLabel = s.stepMode ? "Step-mode" : "Auto-mode";
         const pendingCount = (state.registry ?? []).filter((m) => m.status !== "complete" && m.status !== "parked").length;
@@ -656,7 +657,7 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         // FlatRateContext used by selectAndApplyModel so user-declared
         // flat-rate providers and externalCli auto-detection are respected.
         const { isFlatRateProvider, buildFlatRateContext } = await import("./auto-model-selection.js");
-        const bannerPrefs = loadEffectiveGSDPreferences()?.preferences;
+        const bannerPrefs = loadEffectiveGSDPreferences(base)?.preferences;
         const effectiveProvider = s.autoModeStartModel?.provider ?? ctx.model?.provider;
         const effectivelyEnabled = routingConfig.enabled
             && (routingConfig.allow_flat_rate_providers