Prune deselected workflows during update sync

openspec/changes/simplify-skill-installation/specs/cli-update/spec.md

@@ -160,15 +160,14 @@ The update command SHALL only run inside an initialized OpenSpec project.
 - **THEN** the system SHALL display: "No OpenSpec project found. Run 'openspec init' to set up."
 - **THEN** the system SHALL exit with code 1
 
-### Requirement: Extra workflows preserved
-The update command SHALL NOT remove workflow files that aren't in the current profile.
+### Requirement: Extra workflows synchronized to active profile
+The update command SHALL remove workflow files that are no longer selected in the current profile.
 
-#### Scenario: Extra workflows from previous profile
+#### Scenario: Deselected workflows from previous profile
 - **WHEN** user runs `openspec update`
-- **AND** project has workflows not in current profile (e.g., user switched from custom to core)
-- **THEN** the system SHALL NOT delete those extra workflow files
-- **THEN** the system SHALL only add/update workflows in the current profile
-- **THEN** the system SHALL display a note: "Note: <count> extra workflows not in profile (use `openspec config profile` to manage)"
+- **AND** project has workflows not in current profile (e.g., user switched from custom to core or deselected workflows via `openspec config profile`)
+- **THEN** the system SHALL delete skill and command workflow files for deselected workflows (respecting active delivery mode)
+- **THEN** the system SHALL keep only workflows currently selected in profile
 
 #### Scenario: Delivery change with extra workflows
 - **WHEN** user runs `openspec update`

src/core/profile-sync-drift.ts

@@ -80,11 +80,10 @@ export function getConfiguredToolsForProfileSync(projectPath: string): string[]
 /**
  * Detects if a single tool has profile/delivery drift against the desired state.
  *
- * Note: this function is intentionally scoped to "required artifacts missing"
- * and "artifacts that should not exist for the selected delivery mode".
- * Extra workflows that are outside the desired profile are handled by
- * `hasProjectConfigDrift`, which compares installed workflow IDs against
- * the desired workflow set.
+ * This function covers:
+ * - required artifacts missing for selected workflows
+ * - artifacts that should not exist for the selected delivery mode
+ * - artifacts for workflows that were deselected from the current profile
  */
 export function hasToolProfileOrDeliveryDrift(
   projectPath: string,
@@ -96,6 +95,7 @@ export function hasToolProfileOrDeliveryDrift(
   if (!tool?.skillsDir) return false;
 
   const knownDesiredWorkflows = toKnownWorkflows(desiredWorkflows);
+  const desiredWorkflowSet = new Set<WorkflowId>(knownDesiredWorkflows);
   const skillsDir = path.join(projectPath, tool.skillsDir, 'skills');
   const adapter = CommandAdapterRegistry.get(toolId);
   const shouldGenerateSkills = delivery !== 'commands';
@@ -109,6 +109,16 @@ export function hasToolProfileOrDeliveryDrift(
         return true;
       }
     }
+
+    // Deselecting workflows in a profile should trigger sync.
+    for (const workflow of ALL_WORKFLOWS) {
+      if (desiredWorkflowSet.has(workflow)) continue;
+      const dirName = WORKFLOW_TO_SKILL_DIR[workflow];
+      const skillDir = path.join(skillsDir, dirName);
+      if (fs.existsSync(skillDir)) {
+        return true;
+      }
+    }
   } else {
     for (const workflow of ALL_WORKFLOWS) {
       const dirName = WORKFLOW_TO_SKILL_DIR[workflow];
@@ -127,6 +137,16 @@ export function hasToolProfileOrDeliveryDrift(
         return true;
       }
     }
+
+    // Deselecting workflows in a profile should trigger sync.
+    for (const workflow of ALL_WORKFLOWS) {
+      if (desiredWorkflowSet.has(workflow)) continue;
+      const cmdPath = adapter.getFilePath(workflow);
+      const fullPath = path.isAbsolute(cmdPath) ? cmdPath : path.join(projectPath, cmdPath);
+      if (fs.existsSync(fullPath)) {
+        return true;
+      }
+    }
   } else if (!shouldGenerateCommands && adapter) {
     for (const workflow of ALL_WORKFLOWS) {
       const cmdPath = adapter.getFilePath(workflow);

src/core/update.ts

@@ -176,6 +176,8 @@ export class UpdateCommand {
     const failedTools: Array<{ name: string; error: string }> = [];
     let removedCommandCount = 0;
     let removedSkillCount = 0;
+    let removedDeselectedCommandCount = 0;
+    let removedDeselectedSkillCount = 0;
 
     for (const toolId of toolsToUpdate) {
       const tool = AI_TOOLS.find((t) => t.value === toolId);
@@ -197,6 +199,8 @@ export class UpdateCommand {
             const skillContent = generateSkillContent(template, OPENSPEC_VERSION, transformer);
             await FileSystemUtils.writeFile(skillFile, skillContent);
           }
+
+          removedDeselectedSkillCount += await this.removeUnselectedSkillDirs(skillsDir, desiredWorkflows);
         }
 
         // Delete skill directories if delivery is commands-only
@@ -214,6 +218,12 @@ export class UpdateCommand {
               const commandFile = path.isAbsolute(cmd.path) ? cmd.path : path.join(resolvedProjectPath, cmd.path);
               await FileSystemUtils.writeFile(commandFile, cmd.fileContent);
             }
+
+            removedDeselectedCommandCount += await this.removeUnselectedCommandFiles(
+              resolvedProjectPath,
+              toolId,
+              desiredWorkflows
+            );
           }
         }
 
@@ -247,6 +257,12 @@ export class UpdateCommand {
     if (removedSkillCount > 0) {
       console.log(chalk.dim(`Removed: ${removedSkillCount} skill directories (delivery: commands)`));
     }
+    if (removedDeselectedCommandCount > 0) {
+      console.log(chalk.dim(`Removed: ${removedDeselectedCommandCount} command files (deselected workflows)`));
+    }
+    if (removedDeselectedSkillCount > 0) {
+      console.log(chalk.dim(`Removed: ${removedDeselectedSkillCount} skill directories (deselected workflows)`));
+    }
 
     // 12. Show onboarding message for newly configured tools from legacy upgrade
     if (newlyConfiguredTools.length > 0) {
@@ -378,6 +394,36 @@ export class UpdateCommand {
     return removed;
   }
 
+  /**
+   * Removes skill directories for workflows that are no longer selected in the active profile.
+   * Returns the number of directories removed.
+   */
+  private async removeUnselectedSkillDirs(
+    skillsDir: string,
+    desiredWorkflows: readonly (typeof ALL_WORKFLOWS)[number][]
+  ): Promise<number> {
+    const desiredSet = new Set(desiredWorkflows);
+    let removed = 0;
+
+    for (const workflow of ALL_WORKFLOWS) {
+      if (desiredSet.has(workflow)) continue;
+      const dirName = WORKFLOW_TO_SKILL_DIR[workflow];
+      if (!dirName) continue;
+
+      const skillDir = path.join(skillsDir, dirName);
+      try {
+        if (fs.existsSync(skillDir)) {
+          await fs.promises.rm(skillDir, { recursive: true, force: true });
+          removed++;
+        }
+      } catch {
+        // Ignore errors
+      }
+    }
+
+    return removed;
+  }
+
   /**
    * Removes command files for workflows when delivery changed to skills-only.
    * Returns the number of files removed.
@@ -408,6 +454,40 @@ export class UpdateCommand {
     return removed;
   }
 
+  /**
+   * Removes command files for workflows that are no longer selected in the active profile.
+   * Returns the number of files removed.
+   */
+  private async removeUnselectedCommandFiles(
+    projectPath: string,
+    toolId: string,
+    desiredWorkflows: readonly (typeof ALL_WORKFLOWS)[number][]
+  ): Promise<number> {
+    let removed = 0;
+
+    const adapter = CommandAdapterRegistry.get(toolId);
+    if (!adapter) return 0;
+
+    const desiredSet = new Set(desiredWorkflows);
+
+    for (const workflow of ALL_WORKFLOWS) {
+      if (desiredSet.has(workflow)) continue;
+      const cmdPath = adapter.getFilePath(workflow);
+      const fullPath = path.isAbsolute(cmdPath) ? cmdPath : path.join(projectPath, cmdPath);
+
+      try {
+        if (fs.existsSync(fullPath)) {
+          await fs.promises.unlink(fullPath);
+          removed++;
+        }
+      } catch {
+        // Ignore errors
+      }
+    }
+
+    return removed;
+  }
+
   /**
    * Detect and handle legacy OpenSpec artifacts.
    * Unlike init, update warns but continues if legacy files found in non-interactive mode.

test/core/update.test.ts

@@ -1567,7 +1567,7 @@ content
       consoleSpy.mockRestore();
     });
 
-    it('should display extra workflows note when workflows outside profile exist', async () => {
+    it('should remove workflows outside profile during update sync', async () => {
       // Set core profile (propose, explore, apply, archive)
       setMockConfig({
         featureFlags: {},
@@ -1583,19 +1583,28 @@ content
       // Add a non-core workflow
       await fs.mkdir(path.join(skillsDir, 'openspec-new-change'), { recursive: true });
       await fs.writeFile(path.join(skillsDir, 'openspec-new-change', 'SKILL.md'), 'old');
+      const extraCommandFile = path.join(testDir, '.claude', 'commands', 'opsx', 'new.md');
+      await fs.mkdir(path.dirname(extraCommandFile), { recursive: true });
+      await fs.writeFile(extraCommandFile, 'old');
 
       const consoleSpy = vi.spyOn(console, 'log');
 
       await updateCommand.execute(testDir);
 
-      // Should display note about extra workflows
+      // Deselected workflow artifacts should be removed for both delivery surfaces.
+      expect(await FileSystemUtils.fileExists(
+        path.join(skillsDir, 'openspec-new-change', 'SKILL.md')
+      )).toBe(false);
+      expect(await FileSystemUtils.fileExists(extraCommandFile)).toBe(false);
+
+      // Should report deselected workflow cleanup.
       const calls = consoleSpy.mock.calls.map(call =>
         call.map(arg => String(arg)).join(' ')
       );
-      const hasExtraNote = calls.some(call =>
-        call.includes('extra workflows not in profile')
+      const hasDeselectedRemovalNote = calls.some(call =>
+        call.includes('deselected workflows')
       );
-      expect(hasExtraNote).toBe(true);
+      expect(hasDeselectedRemovalNote).toBe(true);
 
       consoleSpy.mockRestore();
     });