fix(gsd): set slice sequence at all three insertion sites

All slices got sequence=0 because the three code paths that insert
slices never set the sequence column. This made positional ordering
degenerate to alphabetical-by-ID, causing deadlocks when dependency-
free slices were ordered after blocked ones.

Now passes sequence at:
- plan-milestone: array index from agent-ordered params.slices
- reassess-roadmap: existingCount + index for newly added slices
- md-importer: parse order from roadmap content

Closes #3356

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/resources/extensions/gsd/md-importer.ts

@@ -586,7 +586,8 @@ export function migrateHierarchyToDb(basePath: string): {
     // Parse roadmap for slices
     if (!roadmap) continue;
 
-    for (const sliceEntry of roadmap.slices) {
+    for (let si = 0; si < roadmap.slices.length; si++) {
+      const sliceEntry = roadmap.slices[si]!;
       // Per K002: use 'complete' not 'done'
       const sliceStatus = sliceEntry.done ? 'complete' : 'pending';
 
@@ -606,6 +607,7 @@ export function migrateHierarchyToDb(basePath: string): {
         risk: sliceEntry.risk,
         depends: sliceEntry.depends,
         demo: sliceEntry.demo,
+        sequence: si + 1, // Preserve roadmap parse order (#3356)
         planning: {
           goal: plan?.goal ?? '',
         },

src/resources/extensions/gsd/tools/plan-milestone.ts

@@ -256,7 +256,8 @@ export async function handlePlanMilestone(
         boundaryMapMarkdown: params.boundaryMapMarkdown,
       });
 
-      for (const slice of params.slices) {
+      for (let i = 0; i < params.slices.length; i++) {
+        const slice = params.slices[i]!;
         // Preserve completed/done status on re-plan (#2558).
         // Without this, a re-plan after milestone transition would reset
         // already-completed slices back to "pending".
@@ -272,6 +273,7 @@ export async function handlePlanMilestone(
           risk: slice.risk,
           depends: slice.depends,
           demo: slice.demo,
+          sequence: i + 1, // Preserve agent-ordered sequence (#3356)
         });
         upsertSlicePlanning(params.milestoneId, slice.sliceId, {
           goal: slice.goal,

src/resources/extensions/gsd/tools/reassess-roadmap.ts

@@ -186,8 +186,10 @@ export async function handleReassessRoadmap(
         });
       }
 
-      // Insert new slices
-      for (const added of params.sliceChanges.added) {
+      // Insert new slices — assign sequence after existing slices (#3356)
+      const existingCount = getMilestoneSlices(params.milestoneId).length;
+      for (let i = 0; i < params.sliceChanges.added.length; i++) {
+        const added = params.sliceChanges.added[i]!;
         insertSlice({
           id: added.sliceId,
           milestoneId: params.milestoneId,
@@ -196,6 +198,7 @@ export async function handleReassessRoadmap(
           risk: added.risk,
           depends: added.depends,
           demo: added.demo ?? "",
+          sequence: existingCount + i + 1,
         });
       }