fix: Reconcile orphaned changesets when phases are manually deleted

Manually deleting phases left their parent changeset as "applied",
causing the Plan tab to show a stale "Created N phases" banner with
no phases visible.

- deletePhase now checks if all phases from a changeset are gone and
  marks it reverted
- PlanSection filters out dismissed agents so dismissed banners stay
  hidden
- revertChangeSet marks reverted before entity deletion to prevent
  ghost state on partial failure
- deletePhase invalidation now includes listChangeSets

apps/server/db/repositories/change-set-repository.ts

@@ -33,4 +33,10 @@ export interface ChangeSetRepository {
   findByInitiativeId(initiativeId: string): Promise<ChangeSet[]>;
   findByAgentId(agentId: string): Promise<ChangeSet[]>;
   markReverted(id: string): Promise<ChangeSet>;
+
+  /**
+   * Find applied changesets that have a 'create' entry for the given entity.
+   * Used to reconcile changeset status when entities are manually deleted.
+   */
+  findAppliedByCreatedEntity(entityType: string, entityId: string): Promise<ChangeSetWithEntries[]>;
 }

apps/server/db/repositories/drizzle/change-set.ts

@@ -4,7 +4,7 @@
  * Implements ChangeSetRepository interface using Drizzle ORM.
  */
 
-import { eq, desc, asc } from 'drizzle-orm';
+import { eq, desc, asc, and } from 'drizzle-orm';
 import { nanoid } from 'nanoid';
 import type { DrizzleDatabase } from '../../index.js';
 import { changeSets, changeSetEntries, type ChangeSet } from '../../schema.js';
@@ -94,6 +94,32 @@ export class DrizzleChangeSetRepository implements ChangeSetRepository {
       .orderBy(desc(changeSets.createdAt));
   }
 
+  async findAppliedByCreatedEntity(entityType: string, entityId: string): Promise<ChangeSetWithEntries[]> {
+    // Find changeset entries matching the entity
+    const matchingEntries = await this.db
+      .select({ changeSetId: changeSetEntries.changeSetId })
+      .from(changeSetEntries)
+      .where(
+        and(
+          eq(changeSetEntries.entityType, entityType as any),
+          eq(changeSetEntries.entityId, entityId),
+          eq(changeSetEntries.action, 'create'),
+        ),
+      );
+
+    const results: ChangeSetWithEntries[] = [];
+    const seen = new Set<string>();
+    for (const { changeSetId } of matchingEntries) {
+      if (seen.has(changeSetId)) continue;
+      seen.add(changeSetId);
+      const cs = await this.findByIdWithEntries(changeSetId);
+      if (cs && cs.status === 'applied') {
+        results.push(cs);
+      }
+    }
+    return results;
+  }
+
   async markReverted(id: string): Promise<ChangeSet> {
     const [updated] = await this.db
       .update(changeSets)

apps/server/trpc/routers/change-set.ts

@@ -91,6 +91,9 @@ export function changeSetProcedures(publicProcedure: ProcedureBuilder) {
           }
         }
 
+        // Mark reverted FIRST to avoid ghost state if entity deletion fails partway
+        await repo.markReverted(input.id);
+
         // Apply reverts in reverse entry order
         const reversedEntries = [...cs.entries].reverse();
         for (const entry of reversedEntries) {
@@ -159,8 +162,6 @@ export function changeSetProcedures(publicProcedure: ProcedureBuilder) {
           }
         }
 
-        await repo.markReverted(input.id);
-
         ctx.eventBus.emit({
           type: 'changeset:reverted' as const,
           timestamp: new Date(),

apps/server/trpc/routers/phase.ts

@@ -6,7 +6,7 @@ import { TRPCError } from '@trpc/server';
 import { z } from 'zod';
 import type { Phase } from '../../db/schema.js';
 import type { ProcedureBuilder } from '../trpc.js';
-import { requirePhaseRepository, requireTaskRepository, requireBranchManager, requireInitiativeRepository, requireProjectRepository, requireExecutionOrchestrator, requireReviewCommentRepository } from './_helpers.js';
+import { requirePhaseRepository, requireTaskRepository, requireBranchManager, requireInitiativeRepository, requireProjectRepository, requireExecutionOrchestrator, requireReviewCommentRepository, requireChangeSetRepository } from './_helpers.js';
 import { phaseBranchName } from '../../git/branch-naming.js';
 import { ensureProjectClone } from '../../git/project-clones.js';
 
@@ -98,6 +98,29 @@ export function phaseProcedures(publicProcedure: ProcedureBuilder) {
       .mutation(async ({ ctx, input }) => {
         const repo = requirePhaseRepository(ctx);
         await repo.delete(input.id);
+
+        // Reconcile any applied changesets that created this phase.
+        // If all created phases in a changeset are now deleted, mark it reverted.
+        if (ctx.changeSetRepository) {
+          try {
+            const csRepo = requireChangeSetRepository(ctx);
+            const affectedChangeSets = await csRepo.findAppliedByCreatedEntity('phase', input.id);
+            for (const cs of affectedChangeSets) {
+              const createdPhaseIds = cs.entries
+                .filter(e => e.entityType === 'phase' && e.action === 'create')
+                .map(e => e.entityId);
+              const survivingPhases = await Promise.all(
+                createdPhaseIds.map(id => repo.findById(id)),
+              );
+              if (survivingPhases.every(p => p === null)) {
+                await csRepo.markReverted(cs.id);
+              }
+            }
+          } catch {
+            // Best-effort reconciliation — don't fail the delete
+          }
+        }
+
         return { success: true };
       }),
 

apps/web/src/components/execution/PlanSection.tsx

@@ -27,6 +27,7 @@ export function PlanSection({
         (a) =>
           a.mode === "plan" &&
           a.initiativeId === initiativeId &&
+          !a.userDismissedAt &&
           ["running", "waiting_for_input", "idle"].includes(a.status),
       )
       .sort(

apps/web/src/lib/invalidation.ts

@@ -52,7 +52,7 @@ const INVALIDATION_MAP: Partial<Record<MutationName, QueryName[]>> = {
 
   // --- Phases ---
   createPhase: ["listPhases", "listInitiativePhaseDependencies"],
-  deletePhase: ["listPhases", "listInitiativeTasks", "listInitiativePhaseDependencies"],
+  deletePhase: ["listPhases", "listInitiativeTasks", "listInitiativePhaseDependencies", "listChangeSets"],
   updatePhase: ["listPhases", "getPhase"],
   approvePhase: ["listPhases", "listInitiativeTasks"],
   queuePhase: ["listPhases"],