fix(cue): pipeline persistence, save UX, loader resilience, codex stdin banner

Fixes a cluster of Cue pipeline editor bugs around persistence and rendering:

- Pipeline vanish after save: createPipeline assigned timestamp ids; on
  reload subscriptionsToPipelines regenerated name-based ids, leaving the
  saved selectedPipelineId stale and convertToReactFlowNodes skipping every
  pipeline. mergePipelinesWithSavedLayout now validates the saved selection
  against the live pipeline ids and falls back to the first pipeline; a
  live safety-net effect in usePipelineState resets selectedPipelineId to
  null whenever it points at a pipeline that no longer exists.

- Save silently doing nothing: validatePipelines used to skip empty
  pipelines, so 'create N pipelines, click save' returned success without
  writing anything. Empty pipelines are now flagged ('add a trigger and an
  agent before saving') and handleSave refuses to no-op when the editor
  has pipelines but nothing partitions to a root.

- Lost-on-save trust gap: handleSave now write-back-verifies every
  cue:writeYaml by reading the file and comparing bytes, throws on
  mismatch, preserves isDirty on failure, and fires explicit success/
  error toast notifications so the 2-second in-button flash can no longer
  be missed.

- Trigger config caught at load instead of save: pipelineToYaml was happy
  to write a time.scheduled subscription with no schedule_times (or
  time.heartbeat with no interval_minutes, etc.), the loader then rejected
  the entire YAML for every agent in that project root on Cue toggle.
  validatePipelines now mirrors the YAML schema's per-event requirements,
  blocking the bad save up front.

- One bad subscription killing a whole project's config: extracted
  validateSubscription and added partitionValidSubscriptions; loader now
  drops individual invalid subs as warnings instead of failing the entire
  load. Config-level errors (missing subscriptions array, bad settings)
  remain fatal.

- Codex 'Reading additional input from stdin...' in run output: cue
  child processes spawn with stdio[0]='ignore' in local mode so codex
  exec doesn't emit the stdin banner before observing EOF. SSH stdin
  script and SSH small-prompt paths still get a writable pipe.

Also includes editor polish from the working branch: pendingSavedViewportRef
threaded from usePipelineLayout to CuePipelineEditor so viewport restore
waits for ReactFlow to measure nodes (no more empty canvas on first open),
plus PipelineCanvas + AllPipelinesView locking tweaks and matching tests.

Tests: 25,260 passing.

Author: reachrazamair

src/__tests__/main/cue/cue-executor.test.ts

@@ -399,7 +399,10 @@ describe('cue-executor', () => {
 				expect.any(Array),
 				expect.objectContaining({
 					cwd: '/projects/test',
-					stdio: ['pipe', 'pipe', 'pipe'],
+					// Local mode uses 'ignore' for stdin so agents like Codex don't
+					// emit "Reading additional input from stdin..." into the run
+					// output before observing EOF.
+					stdio: ['ignore', 'pipe', 'pipe'],
 				})
 			);
 

src/__tests__/main/cue/cue-process-lifecycle.test.ts

@@ -115,12 +115,14 @@ describe('cue-process-lifecycle', () => {
 			const resultPromise = runProcess('run-1', spec, createOptions());
 			await vi.advanceTimersByTimeAsync(0);
 
+			// Local mode: stdin is `'ignore'` so agents like Codex don't print
+			// "Reading additional input from stdin..." into the run output.
 			expect(mockSpawn).toHaveBeenCalledWith(
 				'claude',
 				['--print', '--', 'test prompt'],
 				expect.objectContaining({
 					cwd: '/projects/test',
-					stdio: ['pipe', 'pipe', 'pipe'],
+					stdio: ['ignore', 'pipe', 'pipe'],
 				})
 			);
 

src/__tests__/main/cue/cue-yaml-loader.test.ts

@@ -334,23 +334,47 @@ subscriptions:
 			}
 		});
 
-		it('returns { ok: false, reason: "invalid", errors } when validation fails', () => {
+		it('skips per-subscription validation errors and surfaces them as warnings', () => {
+			// Lenient loader: a single broken subscription must not block valid
+			// subs in the same YAML. The bad sub is dropped, others load, and
+			// the failure is surfaced as a warning so the user can fix it.
 			mockExistsSync.mockReturnValue(true);
 			mockReadFileSync.mockReturnValue(`
 subscriptions:
   - name: bad-sub
     event: time.heartbeat
     prompt: Hi
+  - name: good-sub
+    event: time.heartbeat
+    prompt: Check status
+    interval_minutes: 5
+`);
+
+			const result = loadCueConfigDetailed('/projects/test');
+
+			expect(result.ok).toBe(true);
+			if (result.ok) {
+				expect(result.config.subscriptions.map((s) => s.name)).toEqual(['good-sub']);
+				expect(result.warnings).toEqual(
+					expect.arrayContaining([
+						expect.stringMatching(/Skipped invalid subscription.*interval_minutes/),
+					])
+				);
+			}
+		});
+
+		it('returns { ok: false, reason: "invalid" } only for config-level errors', () => {
+			mockExistsSync.mockReturnValue(true);
+			mockReadFileSync.mockReturnValue(`
+subscriptions: not-an-array
 `);
-			// Missing interval_minutes for time.heartbeat — validator rejects this.
 
 			const result = loadCueConfigDetailed('/projects/test');
 
 			expect(result.ok).toBe(false);
 			if (!result.ok && result.reason === 'invalid') {
-				expect(result.errors.length).toBeGreaterThan(0);
 				expect(result.errors).toEqual(
-					expect.arrayContaining([expect.stringMatching(/interval_minutes/)])
+					expect.arrayContaining([expect.stringMatching(/subscriptions/)])
 				);
 			}
 		});