gsd-pi 2.80.0-dev.c5f2443b3 → 2.80.0-dev.d4fc28e6b

package/dist/resources/extensions/gsd/bootstrap/agent-end-recovery.js

@@ -1,10 +1,11 @@
+// GSD-2 + src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts - Handles provider and agent-end recovery for GSD auto-mode.
 import { logWarning } from "../workflow-logger.js";
 import { checkDeepProjectSetupAfterTurn, checkAutoStartAfterDiscuss, maybeHandleReadyPhraseWithoutFiles, maybeHandleEmptyIntentTurn, resetEmptyTurnCounter, } from "../guided-flow.js";
 import { clearPathCache } from "../paths.js";
 import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
-import { isSessionSwitchInFlight, resolveAgentEnd } from "../auto/resolve.js";
+import { isSessionSwitchAbortGraceActive, isSessionSwitchInFlight, resolveAgentEnd, resolveAgentEndCancelled, } from "../auto/resolve.js";
 import { resolveModelId } from "../auto-model-selection.js";
 import { resolveProjectRoot } from "../worktree.js";
 import { clearDiscussionFlowState } from "./write-gate.js";
@@ -47,6 +48,89 @@ export function _buildAbortedPauseContext(lastMsg) {
         isTransient: true,
     };
 }
+export function isUserInitiatedAbortMessage(message) {
+    if (!message)
+        return false;
+    return /\b(?:claude code process aborted by user|request aborted by user|process aborted by user)\b/i.test(message);
+}
+function isBareClaudeCodeSessionSwitchAbortMarker(message) {
+    if (!message)
+        return false;
+    const normalized = message.trim().replace(/\s+/g, " ").toLowerCase();
+    return normalized === "claude code process aborted by user"
+        || normalized === "request aborted by user"
+        || normalized === "process aborted by user"
+        || normalized === "claude code stream aborted by caller";
+}
+function readAssistantTextContent(content) {
+    if (!Array.isArray(content))
+        return "";
+    return content
+        .map((block) => {
+        if (!block || typeof block !== "object")
+            return "";
+        const text = block.text;
+        return typeof text === "string" ? text : "";
+    })
+        .filter(Boolean)
+        .join("\n");
+}
+export function isClaudeCodeSessionSwitchAbortMessage(lastMsg) {
+    if (!lastMsg || typeof lastMsg !== "object")
+        return false;
+    const m = lastMsg;
+    const carriers = [
+        m.errorMessage ? String(m.errorMessage) : "",
+        readAssistantTextContent(m.content),
+    ].filter((value) => value.trim().length > 0);
+    if ((m.stopReason === "error" || m.stopReason === "aborted") && carriers.length > 0) {
+        return carriers.every(isBareClaudeCodeSessionSwitchAbortMarker);
+    }
+    return false;
+}
+/**
+ * Resolve an agent_end event observed while a session switch is in flight.
+ *
+ * #5538-followup: When `newSession()` aborts an in-flight stream as part of a
+ * session transition (run-unit.ts:63 → _settleCurrentTurnForSessionTransition
+ * → agent.abort()), the SDK emits "Claude Code process aborted by user" or
+ * "Request aborted by user" against the previous unit's turn. The previous
+ * code path treated that as a user cancellation and propagated it to the next
+ * unit via the pending-switch-cancellation queue, killing auto-mode with
+ * "Auto-mode stopped — Unit aborted: Claude Code process aborted by user"
+ * even though no user input occurred.
+ *
+ * Claude Code abort markers are intentionally ignored when the abort fires
+ * while the session-switch is in flight: the abort is the expected side-effect
+ * of the transition, not a user signal. Other branches (genuine `stopReason
+ * === "aborted"` with diagnostic content/errorMessage) preserve the prior
+ * behavior.
+ */
+export function _handleSessionSwitchAgentEnd(lastMsg, resolveCancelled) {
+    if (!lastMsg || typeof lastMsg !== "object")
+        return;
+    const m = lastMsg;
+    if (isClaudeCodeSessionSwitchAbortMessage(m)) {
+        // Internal abort from in-flight session transition — drop on the floor.
+        return;
+    }
+    if (m.stopReason === "error") {
+        const rawErrorMsg = m.errorMessage ? String(m.errorMessage) : "";
+        if (isBareClaudeCodeSessionSwitchAbortMarker(rawErrorMsg)) {
+            // Internal abort from in-flight session transition — drop on the floor.
+            return;
+        }
+        return;
+    }
+    if (m.stopReason === "aborted") {
+        const content = m.content;
+        const hasEmptyContent = Array.isArray(content) && content.length === 0;
+        const hasErrorMessage = !!m.errorMessage;
+        if (!hasEmptyContent || hasErrorMessage) {
+            resolveCancelled(_buildAbortedPauseContext(m));
+        }
+    }
+}
 async function pauseTransientWithBackoff(cls, pi, ctx, errorDetail, isRateLimit) {
     retryState.consecutiveTransientCount += 1;
     const baseRetryAfterMs = "retryAfterMs" in cls ? cls.retryAfterMs : 15_000;
@@ -112,9 +196,17 @@ export async function handleAgentEnd(pi, event, ctx) {
         return;
     if (!isAutoActive())
         return;
-    if (isSessionSwitchInFlight())
-        return;
     const lastMsg = event.messages[event.messages.length - 1];
+    if (isSessionSwitchInFlight()) {
+        _handleSessionSwitchAgentEnd(lastMsg, resolveAgentEndCancelled);
+        return;
+    }
+    if (isSessionSwitchAbortGraceActive() && isClaudeCodeSessionSwitchAbortMessage(lastMsg)) {
+        // Claude Code can report the abort from `newSession()` a few hundred ms
+        // after the guard drops. That event belongs to the old turn; do not let it
+        // cancel the freshly-dispatched unit.
+        return;
+    }
     if (lastMsg && "stopReason" in lastMsg && lastMsg.stopReason === "aborted") {
         // Empty content with aborted stopReason is a non-fatal agent stop (the LLM
         // chose to end without producing output). Only pause on genuine fatal aborts
@@ -150,6 +242,14 @@ export async function handleAgentEnd(pi, event, ctx) {
         // is in the assistant message text content. Fall back to content when
         // errorMessage looks uninformative.
         const rawErrorMsg = ("errorMessage" in lastMsg && lastMsg.errorMessage) ? String(lastMsg.errorMessage) : "";
+        if (isUserInitiatedAbortMessage(rawErrorMsg)) {
+            resolveAgentEndCancelled({
+                message: rawErrorMsg,
+                category: "aborted",
+                isTransient: false,
+            });
+            return;
+        }
         const isUseless = !rawErrorMsg || /^(success|ok|true|error|unknown)$/i.test(rawErrorMsg.trim());
         // #3588: When errorMessage is uninformative, extract the real error from
         // the assistant message text content for display purposes only.

package/dist/resources/extensions/gsd/bootstrap/db-tools.js

@@ -11,6 +11,12 @@ import { incrementLegacyTelemetry } from "../legacy-telemetry.js";
 async function loadWorkflowExecutors() {
     return import("../tools/workflow-tool-executors.js");
 }
+function toolWorkspaceRoot(ctx) {
+    if (ctx && typeof ctx === "object" && typeof ctx.cwd === "string") {
+        return ctx.cwd;
+    }
+    return process.cwd();
+}
 /**
  * Register an alias tool that shares the same execute function as its canonical counterpart.
  * The alias description and promptGuidelines direct the LLM to prefer the canonical name.
@@ -31,8 +37,8 @@ function registerAlias(pi, toolDef, aliasName, canonicalName) {
         execute,
     });
 }
-function requirementRootWriteGuard(operation) {
-    const guard = shouldBlockRootArtifactSaveInSnapshot(loadWriteGateSnapshot(process.cwd()), "REQUIREMENTS");
+function requirementRootWriteGuard(operation, basePath) {
+    const guard = shouldBlockRootArtifactSaveInSnapshot(loadWriteGateSnapshot(basePath), "REQUIREMENTS");
     if (!guard.block)
         return null;
     return {
@@ -56,7 +62,8 @@ function readDetails(result) {
 export function registerDbTools(pi) {
     // ─── gsd_decision_save (formerly gsd_save_decision) ─────────────────────
     const decisionSaveExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot save decision." }],
@@ -73,7 +80,7 @@ export function registerDbTools(pi) {
                 revisable: params.revisable,
                 when_context: params.when_context,
                 made_by: params.made_by,
-            }, process.cwd());
+            }, basePath);
             return {
                 content: [{ type: "text", text: `Saved decision ${id}` }],
                 details: { operation: "save_decision", id },
@@ -140,10 +147,11 @@ export function registerDbTools(pi) {
     registerAlias(pi, decisionSaveTool, "gsd_save_decision", "gsd_decision_save");
     // ─── gsd_requirement_update (formerly gsd_update_requirement) ───────────
     const requirementUpdateExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const gateBlock = requirementRootWriteGuard("update_requirement");
+        const basePath = toolWorkspaceRoot(_ctx);
+        const gateBlock = requirementRootWriteGuard("update_requirement", basePath);
         if (gateBlock)
             return gateBlock;
-        const dbAvailable = await ensureDbOpen();
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot update requirement." }],
@@ -165,7 +173,7 @@ export function registerDbTools(pi) {
                 updates.primary_owner = params.primary_owner;
             if (params.supporting_slices !== undefined)
                 updates.supporting_slices = params.supporting_slices;
-            await updateRequirementInDb(params.id, updates, process.cwd());
+            await updateRequirementInDb(params.id, updates, basePath);
             return {
                 content: [{ type: "text", text: `Updated requirement ${params.id}` }],
                 details: { operation: "update_requirement", id: params.id },
@@ -225,10 +233,11 @@ export function registerDbTools(pi) {
     registerAlias(pi, requirementUpdateTool, "gsd_update_requirement", "gsd_requirement_update");
     // ─── gsd_requirement_save ─────────────────────────────────────────────
     const requirementSaveExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const gateBlock = requirementRootWriteGuard("save_requirement");
+        const basePath = toolWorkspaceRoot(_ctx);
+        const gateBlock = requirementRootWriteGuard("save_requirement", basePath);
         if (gateBlock)
             return gateBlock;
-        const dbAvailable = await ensureDbOpen();
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot save requirement." }],
@@ -247,7 +256,7 @@ export function registerDbTools(pi) {
                 supporting_slices: params.supporting_slices,
                 validation: params.validation,
                 notes: params.notes,
-            }, process.cwd());
+            }, basePath);
             return {
                 content: [{ type: "text", text: `Saved requirement ${result.id}` }],
                 details: { operation: "save_requirement", id: result.id },
@@ -324,7 +333,7 @@ export function registerDbTools(pi) {
     // ─── gsd_summary_save (formerly gsd_save_summary) ──────────────────────
     const summarySaveExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeSummarySave } = await loadWorkflowExecutors();
-        return executeSummarySave(params, process.cwd());
+        return executeSummarySave(params, toolWorkspaceRoot(_ctx));
     };
     const summarySaveTool = {
         name: "gsd_summary_save",
@@ -373,23 +382,23 @@ export function registerDbTools(pi) {
     // ─── gsd_milestone_generate_id (formerly gsd_generate_milestone_id) ────
     const milestoneGenerateIdExecute = async (_toolCallId, _params, _signal, _onUpdate, _ctx) => {
         try {
+            const basePath = toolWorkspaceRoot(_ctx);
             // Claim a reserved ID if the guided-flow already previewed one to the user.
             // This guarantees the ID shown in the UI matches the one materialised on disk.
             const { claimReservedId, findMilestoneIds, getReservedMilestoneIds, nextMilestoneId } = await import("../guided-flow.js");
             const reserved = claimReservedId();
             if (reserved) {
-                await ensureMilestoneDbRow(reserved);
+                await ensureMilestoneDbRow(reserved, basePath);
                 return {
                     content: [{ type: "text", text: reserved }],
                     details: { operation: "generate_milestone_id", id: reserved, source: "reserved" },
                 };
             }
-            const basePath = process.cwd();
             const existingIds = findMilestoneIds(basePath);
-            const uniqueEnabled = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
+            const uniqueEnabled = !!loadEffectiveGSDPreferences(basePath)?.preferences?.unique_milestone_ids;
             const allIds = [...new Set([...existingIds, ...getReservedMilestoneIds()])];
             const newId = nextMilestoneId(allIds, uniqueEnabled);
-            await ensureMilestoneDbRow(newId);
+            await ensureMilestoneDbRow(newId, basePath);
             return {
                 content: [{ type: "text", text: newId }],
                 details: { operation: "generate_milestone_id", id: newId, existingCount: existingIds.length, uniqueEnabled },
@@ -409,8 +418,8 @@ export function registerDbTools(pi) {
      * later writes the full row. Silently skips if the DB isn't available yet
      * (pre-migration).
      */
-    async function ensureMilestoneDbRow(milestoneId) {
-        const dbAvailable = await ensureDbOpen();
+    async function ensureMilestoneDbRow(milestoneId, basePath) {
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable)
             return;
         try {
@@ -455,7 +464,7 @@ export function registerDbTools(pi) {
     // ─── gsd_plan_milestone (gsd_milestone_plan alias) ─────────────────────
     const planMilestoneExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executePlanMilestone } = await loadWorkflowExecutors();
-        return executePlanMilestone(params, process.cwd());
+        return executePlanMilestone(params, toolWorkspaceRoot(_ctx));
     };
     const planMilestoneTool = {
         name: "gsd_plan_milestone",
@@ -520,7 +529,7 @@ export function registerDbTools(pi) {
     // ─── gsd_plan_slice (gsd_slice_plan alias) ─────────────────────────────
     const planSliceExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executePlanSlice } = await loadWorkflowExecutors();
-        return executePlanSlice(params, process.cwd());
+        return executePlanSlice(params, toolWorkspaceRoot(_ctx));
     };
     const planSliceTool = {
         name: "gsd_plan_slice",
@@ -564,7 +573,8 @@ export function registerDbTools(pi) {
     registerAlias(pi, planSliceTool, "gsd_slice_plan", "gsd_plan_slice");
     // ─── gsd_plan_task (gsd_task_plan alias) ───────────────────────────────
     const planTaskExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot plan task." }],
@@ -573,7 +583,7 @@ export function registerDbTools(pi) {
         }
         try {
             const { handlePlanTask } = await import("../tools/plan-task.js");
-            const result = await handlePlanTask(params, process.cwd());
+            const result = await handlePlanTask(params, basePath);
             if ("error" in result) {
                 return {
                     content: [{ type: "text", text: `Error planning task: ${result.error}` }],
@@ -634,7 +644,7 @@ export function registerDbTools(pi) {
     // ─── gsd_task_complete (gsd_complete_task alias) ────────────────────────
     const taskCompleteExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeTaskComplete } = await loadWorkflowExecutors();
-        return executeTaskComplete(params, process.cwd());
+        return executeTaskComplete(params, toolWorkspaceRoot(_ctx));
     };
     const taskCompleteTool = {
         name: "gsd_task_complete",
@@ -697,7 +707,7 @@ export function registerDbTools(pi) {
     // ─── gsd_slice_complete (gsd_complete_slice alias) ─────────────────────
     const sliceCompleteExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeSliceComplete } = await loadWorkflowExecutors();
-        return executeSliceComplete(params, process.cwd());
+        return executeSliceComplete(params, toolWorkspaceRoot(_ctx));
     };
     const sliceCompleteTool = {
         name: "gsd_slice_complete",
@@ -777,7 +787,8 @@ export function registerDbTools(pi) {
     registerAlias(pi, sliceCompleteTool, "gsd_complete_slice", "gsd_slice_complete");
     // ─── gsd_skip_slice (#3477 / #3487) ───────────────────────────────────
     const skipSliceExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot skip slice." }],
@@ -806,7 +817,6 @@ export function registerDbTools(pi) {
             // Rebuild STATE.md so it reflects the skip immediately (#3477).
             // Without this, /gsd auto reads stale STATE.md and resumes the skipped slice.
             try {
-                const basePath = process.cwd();
                 const { rebuildState } = await import("../doctor.js");
                 await rebuildState(basePath);
             }
@@ -862,7 +872,7 @@ export function registerDbTools(pi) {
     // ─── gsd_complete_milestone ────────────────────────────────────────────
     const milestoneCompleteExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeCompleteMilestone } = await loadWorkflowExecutors();
-        return executeCompleteMilestone(params, process.cwd());
+        return executeCompleteMilestone(params, toolWorkspaceRoot(_ctx));
     };
     const milestoneCompleteTool = {
         name: "gsd_complete_milestone",
@@ -903,7 +913,7 @@ export function registerDbTools(pi) {
     // ─── gsd_validate_milestone (gsd_milestone_validate alias) ─────────────
     const milestoneValidateExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeValidateMilestone } = await loadWorkflowExecutors();
-        return executeValidateMilestone(params, process.cwd());
+        return executeValidateMilestone(params, toolWorkspaceRoot(_ctx));
     };
     const milestoneValidateTool = {
         name: "gsd_validate_milestone",
@@ -936,7 +946,7 @@ export function registerDbTools(pi) {
     // ─── gsd_replan_slice (gsd_slice_replan alias) ─────────────────────────
     const replanSliceExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeReplanSlice } = await loadWorkflowExecutors();
-        return executeReplanSlice(params, process.cwd());
+        return executeReplanSlice(params, toolWorkspaceRoot(_ctx));
     };
     const replanSliceTool = {
         name: "gsd_replan_slice",
@@ -979,7 +989,7 @@ export function registerDbTools(pi) {
     // ─── gsd_reassess_roadmap (gsd_roadmap_reassess alias) ─────────────────
     const reassessRoadmapExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeReassessRoadmap } = await loadWorkflowExecutors();
-        return executeReassessRoadmap(params, process.cwd());
+        return executeReassessRoadmap(params, toolWorkspaceRoot(_ctx));
     };
     const reassessRoadmapTool = {
         name: "gsd_reassess_roadmap",
@@ -1027,7 +1037,8 @@ export function registerDbTools(pi) {
     // ─── gsd_task_reopen (gsd_reopen_task alias) ───────────────────────────
     // Single-writer v3, Stream 3: reversibility tools for closed units.
     const reopenTaskExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot reopen task." }],
@@ -1036,7 +1047,7 @@ export function registerDbTools(pi) {
         }
         try {
             const { handleReopenTask } = await import("../tools/reopen-task.js");
-            const result = await handleReopenTask(params, process.cwd());
+            const result = await handleReopenTask(params, basePath);
             if ("error" in result) {
                 return {
                     content: [{ type: "text", text: `Error reopening task: ${result.error}` }],
@@ -1089,7 +1100,8 @@ export function registerDbTools(pi) {
     registerAlias(pi, reopenTaskTool, "gsd_reopen_task", "gsd_task_reopen");
     // ─── gsd_slice_reopen (gsd_reopen_slice alias) ─────────────────────────
     const reopenSliceExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot reopen slice." }],
@@ -1098,7 +1110,7 @@ export function registerDbTools(pi) {
         }
         try {
             const { handleReopenSlice } = await import("../tools/reopen-slice.js");
-            const result = await handleReopenSlice(params, process.cwd());
+            const result = await handleReopenSlice(params, basePath);
             if ("error" in result) {
                 return {
                     content: [{ type: "text", text: `Error reopening slice: ${result.error}` }],
@@ -1151,7 +1163,8 @@ export function registerDbTools(pi) {
     registerAlias(pi, reopenSliceTool, "gsd_reopen_slice", "gsd_slice_reopen");
     // ─── gsd_milestone_reopen (gsd_reopen_milestone alias) ─────────────────
     const reopenMilestoneExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
-        const dbAvailable = await ensureDbOpen();
+        const basePath = toolWorkspaceRoot(_ctx);
+        const dbAvailable = await ensureDbOpen(basePath);
         if (!dbAvailable) {
             return {
                 content: [{ type: "text", text: "Error: GSD database is not available. Cannot reopen milestone." }],
@@ -1160,7 +1173,7 @@ export function registerDbTools(pi) {
         }
         try {
             const { handleReopenMilestone } = await import("../tools/reopen-milestone.js");
-            const result = await handleReopenMilestone(params, process.cwd());
+            const result = await handleReopenMilestone(params, basePath);
             if ("error" in result) {
                 return {
                     content: [{ type: "text", text: `Error reopening milestone: ${result.error}` }],
@@ -1212,7 +1225,7 @@ export function registerDbTools(pi) {
     // ─── gsd_save_gate_result ──────────────────────────────────────────────
     const saveGateResultExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
         const { executeSaveGateResult } = await loadWorkflowExecutors();
-        return executeSaveGateResult(params, process.cwd());
+        return executeSaveGateResult(params, toolWorkspaceRoot(_ctx));
     };
     const saveGateResultTool = {
         name: "gsd_save_gate_result",

package/dist/resources/extensions/gsd/bootstrap/dynamic-tools.js

@@ -4,6 +4,12 @@ import { createBashTool, createEditTool, createReadTool, createWriteTool } from
 import { DEFAULT_BASH_TIMEOUT_SECS } from "../constants.js";
 import { setLogBasePath, logWarning } from "../workflow-logger.js";
 import { resolveGsdPathContract } from "../paths.js";
+function resolveToolWorkspaceRoot(ctx) {
+    if (ctx && typeof ctx === "object" && typeof ctx.cwd === "string") {
+        return ctx.cwd;
+    }
+    return process.cwd();
+}
 /**
  * Resolve the correct DB path for the current working directory.
  * If `basePath` is inside a `.gsd/worktrees/<MID>/` directory, returns
@@ -45,16 +51,20 @@ export async function ensureDbOpen(basePath = process.cwd()) {
 }
 export function registerDynamicTools(pi) {
     const baseBash = createBashTool(process.cwd(), {
-        spawnHook: (ctx) => ({ ...ctx, cwd: process.cwd() }),
+        spawnHook: (ctx) => ctx,
     });
     const dynamicBash = {
         ...baseBash,
         execute: async (toolCallId, params, signal, onUpdate, ctx) => {
+            const basePath = resolveToolWorkspaceRoot(ctx);
+            const fresh = createBashTool(basePath, {
+                spawnHook: (spawnCtx) => ({ ...spawnCtx, cwd: basePath }),
+            });
             const paramsWithTimeout = {
                 ...params,
                 timeout: params.timeout ?? DEFAULT_BASH_TIMEOUT_SECS,
             };
-            return baseBash.execute(toolCallId, paramsWithTimeout, signal, onUpdate, ctx);
+            return fresh.execute(toolCallId, paramsWithTimeout, signal, onUpdate, ctx);
         },
     };
     pi.registerTool(dynamicBash);
@@ -62,7 +72,7 @@ export function registerDynamicTools(pi) {
     pi.registerTool({
         ...baseWrite,
         execute: async (toolCallId, params, signal, onUpdate, ctx) => {
-            const fresh = createWriteTool(process.cwd());
+            const fresh = createWriteTool(resolveToolWorkspaceRoot(ctx));
             return fresh.execute(toolCallId, params, signal, onUpdate, ctx);
         },
     });
@@ -70,7 +80,7 @@ export function registerDynamicTools(pi) {
     pi.registerTool({
         ...baseRead,
         execute: async (toolCallId, params, signal, onUpdate, ctx) => {
-            const fresh = createReadTool(process.cwd());
+            const fresh = createReadTool(resolveToolWorkspaceRoot(ctx));
             return fresh.execute(toolCallId, params, signal, onUpdate, ctx);
         },
     });
@@ -78,7 +88,7 @@ export function registerDynamicTools(pi) {
     pi.registerTool({
         ...baseEdit,
         execute: async (toolCallId, params, signal, onUpdate, ctx) => {
-            const fresh = createEditTool(process.cwd());
+            const fresh = createEditTool(resolveToolWorkspaceRoot(ctx));
             return fresh.execute(toolCallId, params, signal, onUpdate, ctx);
         },
     });

package/dist/resources/extensions/gsd/bootstrap/exec-tools.js

@@ -3,21 +3,40 @@
 // Exposes the Context Mode runtime tools in-process. Default-on; opt out with
 // `context_mode.enabled: false` in preferences.
 import { Type } from "@sinclair/typebox";
+function toolWorkspaceRoot(ctx) {
+    if (ctx && typeof ctx === "object" && typeof ctx.cwd === "string") {
+        return ctx.cwd;
+    }
+    return process.cwd();
+}
+async function loadContextModePreferences(baseDir) {
+    const [{ loadEffectiveGSDPreferences }, { logWarning }] = await Promise.all([
+        import("../preferences.js"),
+        import("../workflow-logger.js"),
+    ]);
+    try {
+        return loadEffectiveGSDPreferences(baseDir)?.preferences ?? null;
+    }
+    catch (err) {
+        logWarning("tool", `Context Mode tool could not load preferences: ${err instanceof Error ? err.message : String(err)}`);
+        return null;
+    }
+}
 export function registerExecTools(pi) {
     pi.registerTool({
         name: "gsd_exec",
         label: "Exec (Sandboxed)",
-        description: "Run a short script (bash/node/python) in a subprocess. Full stdout/stderr persist to " +
+        description: "Run a short script (bash/node/python) in a subprocess. Capped stdout/stderr and metadata persist to " +
             ".gsd/exec/<id>.{stdout,stderr,meta.json}; only a short digest returns in context. Use " +
             "this instead of reading many files or emitting large tool outputs — e.g. have the script " +
             "count/grep/summarize and log the finding. Enabled by default; opt out via " +
             "preferences.context_mode.enabled=false.",
-        promptSnippet: "Run a bash/node/python script in a sandbox; full output is saved to disk and only a digest returns",
+        promptSnippet: "Run a bash/node/python script in a sandbox; capped output is saved to disk and only a digest returns",
         promptGuidelines: [
             "Prefer gsd_exec for analyses that would otherwise read >3 files or produce large tool output.",
             "Write scripts that log the finding (counts, matches, summaries) rather than raw dumps.",
             "The digest is the last ~300 chars of stdout — size your log output accordingly.",
-            "Need the full output? Read the stdout_path returned in details (file on local disk).",
+            "Need persisted output? Read the stdout_path returned in details (file on local disk).",
         ],
         parameters: Type.Object({
             runtime: Type.Union([Type.Literal("bash"), Type.Literal("node"), Type.Literal("python")], { description: "Interpreter: bash (-c), node (-e), or python3 (-c)." }),
@@ -30,21 +49,11 @@ export function registerExecTools(pi) {
             })),
         }),
         async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
-            const [{ executeGsdExec }, { loadEffectiveGSDPreferences }, { logWarning }] = await Promise.all([
-                import("../tools/exec-tool.js"),
-                import("../preferences.js"),
-                import("../workflow-logger.js"),
-            ]);
-            let prefs = null;
-            try {
-                prefs = loadEffectiveGSDPreferences();
-            }
-            catch (err) {
-                logWarning("tool", `gsd_exec could not load preferences: ${err instanceof Error ? err.message : String(err)}`);
-            }
+            const { executeGsdExec } = await import("../tools/exec-tool.js");
+            const baseDir = toolWorkspaceRoot(_ctx);
             return executeGsdExec(params, {
-                baseDir: process.cwd(),
-                preferences: prefs?.preferences ?? null,
+                baseDir,
+                preferences: await loadContextModePreferences(baseDir),
             });
         },
     });
@@ -56,7 +65,7 @@ export function registerExecTools(pi) {
         promptSnippet: "Search prior gsd_exec runs by substring, runtime, or failing-only filter",
         promptGuidelines: [
             "Use this before re-running an expensive analysis — the prior run's stdout file may still answer.",
-            "The preview shows the trailing ~300 chars of stdout; read stdout_path for the full transcript.",
+            "The preview shows the trailing ~300 chars of stdout; read stdout_path for persisted output.",
         ],
         parameters: Type.Object({
             query: Type.Optional(Type.String({ description: "Substring matched against id and purpose (case-insensitive)." })),
@@ -68,8 +77,10 @@ export function registerExecTools(pi) {
         }),
         async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
             const { executeExecSearch } = await import("../tools/exec-search-tool.js");
+            const baseDir = toolWorkspaceRoot(_ctx);
             return executeExecSearch(params, {
-                baseDir: process.cwd(),
+                baseDir,
+                preferences: await loadContextModePreferences(baseDir),
             });
         },
     });
@@ -87,8 +98,10 @@ export function registerExecTools(pi) {
         parameters: Type.Object({}),
         async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
             const { executeResume } = await import("../tools/resume-tool.js");
+            const baseDir = toolWorkspaceRoot(_ctx);
             return executeResume(params, {
-                baseDir: process.cwd(),
+                baseDir,
+                preferences: await loadContextModePreferences(baseDir),
             });
         },
     });

package/dist/resources/extensions/gsd/bootstrap/journal-tools.js

@@ -1,6 +1,12 @@
 import { Type } from "@sinclair/typebox";
 import { queryJournal } from "../journal.js";
 import { logWarning } from "../workflow-logger.js";
+function toolWorkspaceRoot(ctx) {
+    if (ctx && typeof ctx === "object" && typeof ctx.cwd === "string") {
+        return ctx.cwd;
+    }
+    return process.cwd();
+}
 export function registerJournalTools(pi) {
     pi.registerTool({
         name: "gsd_journal_query",
@@ -37,7 +43,7 @@ export function registerJournalTools(pi) {
                     filters.after = params.after;
                 if (params.before !== undefined)
                     filters.before = params.before;
-                const entries = queryJournal(process.cwd(), filters);
+                const entries = queryJournal(toolWorkspaceRoot(_ctx), filters);
                 const limited = entries.slice(0, params.limit ?? 100);
                 if (limited.length === 0) {
                     return {