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)