fix: harden workflows, configuration, and desktop UX (#246)

## Related Issue

N/A — maintainer-directed hardening batch.

## Problem

Several agent, configuration, desktop, and Web paths still had
reliability or presentation gaps. Dynamic Workflow could lose truthful
progress or recovery details after partial failures and used different
subagent-selection paths across entry points. Configuration saves could
expose transient reads, desktop launches could use the wrong executable
order, and installer and tool-row presentation remained inconsistent.

## What changed

- Route Dynamic Workflow, Tower, and Session Init through the shared
subagent spawn planner; validate routing inputs and preserve
created-child recovery details.
- Keep configured workflow capacity authoritative during rate limits,
frame child results safely, and recover truthful row counts and statuses
from partial events.
- Keep built-in prompts free of clock-derived text while preserving
`${now}` for custom templates; stabilize configuration reads and
validate Dynamic Workflow environment overrides.
- Use login-shell executable order for desktop-launched tools and brand
the macOS DMG with a drag-to-Applications layout.
- Align Web tool icons and completion indicators, preserve distinct
workflow result rows, and rebuild the committed Web bundle.

### Review focus

- Shared subagent selection, forced-policy precedence, fork validation,
cancellation rollback, and binding preservation.
- Rate-limit recovery, startup failures, active-versus-queued
attribution, and partial-result rendering.
- Desktop PATH ordering, DMG packaging, configuration-save stability,
and generated Web asset provenance.

### Verification

- `pnpm test` — 1,231 files and 20,843 tests passed; 12 files and 79
tests skipped; 3 expected failures and 2 todos.
- Final `agent-core-v2` suite — 350 files and 5,855 tests passed.
- Pre-push changed suite — 418 files and 7,147 tests passed; 2 files and
2 tests skipped; 1 todo.
- `pnpm build`, `pnpm typecheck`, and `pnpm lint` passed; lint reports 0
errors and 3,329 existing warnings.
- Docs build, Web asset freshness, Sherif, flake workspace sync,
changeset validation, and diff checks passed.

## Checklist

- [x] I have read the
[CONTRIBUTING](https://github.com/PyModel/pythinker-code/blob/main/CONTRIBUTING.md)
document.
- [x] Related issue: N/A — maintainer-directed hardening batch.
- [x] I have added tests that prove the changes work.
- [x] Ran `gen-changesets`; the existing CLI and desktop patch
changesets cover user-visible changes, with no new breaking change.
- [x] Ran `gen-docs`; custom-template compatibility and Dynamic Workflow
controls are documented, and the docs build passed.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **New Features**
* Added dynamic workflow concurrency controls through configuration and
environment settings.
* Improved subagent spawning, cancellation, recovery, and progress
tracking.
  * Desktop tools now use the login shell’s executable path order.

* **Bug Fixes**
* Fixed tool-call icons and completion indicators appearing misaligned.
* Preserved models and providers while configuration files are being
saved.
  * Improved recovery of partially completed workflow results.
  * Added safer handling for encoded workflow output and file updates.

* **Style**
  * Updated macOS installer branding and layout.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: elkaix

.changeset/align-tool-row-icons.md

@@ -0,0 +1,5 @@
+---
+"@pymodel/pythinker-code": patch
+---
+
+Align tool-call icons and completion indicators with their labels in web conversations.

.changeset/brand-macos-installer.md

@@ -0,0 +1,5 @@
+---
+"@pymodel/pythinker-desktop": patch
+---
+
+Brand the macOS installer with the Pythinker Code drag-to-Applications layout.

.changeset/harden-dynamic-workflow-recovery.md

@@ -0,0 +1,5 @@
+---
+"@pymodel/pythinker-code": patch
+---
+
+Fix Dynamic Workflow subagent selection, recovery, and progress reporting during partial failures.

.changeset/stabilize-config-file-reads.md

@@ -0,0 +1,5 @@
+---
+"@pymodel/pythinker-code": patch
+---
+
+Fix models and providers briefly disappearing when an external editor saves the configuration.

.changeset/use-desktop-login-shell-path.md

@@ -0,0 +1,5 @@
+---
+"@pymodel/pythinker-code": patch
+---
+
+Use the login shell's executable order for tools started by the desktop app.

apps/desktop/build/background.png

@@ -70,6 +70,7 @@
       ]
     },
     "dmg": {
+      "background": "build/background.png",
       "sign": true,
       "title": "Pythinker ${version}",
       "window": {
@@ -80,14 +81,28 @@
       "contents": [
         {
           "x": 180,
-          "y": 200,
+          "y": 250,
           "type": "file"
         },
         {
           "x": 480,
-          "y": 200,
+          "y": 250,
           "type": "link",
           "path": "/Applications"
+        },
+        {
+          "name": ".background.png",
+          "path": "build/background.png",
+          "type": "file",
+          "x": 760,
+          "y": 520
+        },
+        {
+          "name": ".VolumeIcon.icns",
+          "path": "dist/.icon-icns/icon.icns",
+          "type": "file",
+          "x": 760,
+          "y": 520
         }
       ]
     },

apps/desktop/package.json

@@ -9,7 +9,9 @@ interface DesktopPackage {
     readonly afterPack: string
     readonly appId: string
     readonly dmg: {
+      readonly background: string
       readonly contents: readonly {
+        readonly name?: string
         readonly path?: string
         readonly type: string
         readonly x: number
@@ -135,11 +137,39 @@ describe('desktop packaging configuration', () => {
       window: { height: 400, width: 660 },
     })
     expect(desktopPackage.build.dmg.contents).toEqual([
-      { x: 180, y: 200, type: 'file' },
-      { x: 480, y: 200, type: 'link', path: '/Applications' },
+      { x: 180, y: 250, type: 'file' },
+      { x: 480, y: 250, type: 'link', path: '/Applications' },
+      {
+        name: '.background.png',
+        path: 'build/background.png',
+        type: 'file',
+        x: 760,
+        y: 520,
+      },
+      {
+        name: '.VolumeIcon.icns',
+        path: 'dist/.icon-icns/icon.icns',
+        type: 'file',
+        x: 760,
+        y: 520,
+      },
     ])
   })
 
+  it('uses the branded 660x400 macOS DMG background', () => {
+    const backgroundPath = resolve(desktopRoot, 'build/background.png')
+
+    expect(desktopPackage.build.dmg.background).toBe('build/background.png')
+    expect(existsSync(backgroundPath)).toBe(true)
+
+    const background = readFileSync(backgroundPath)
+    expect(createHash('sha256').update(background).digest('hex'))
+      .toBe('95e8b785add86919d269b198844d8a903280190f8fd33d5f8ffdca404c113fa8')
+    expect(background.subarray(0, 8).toString('hex')).toBe('89504e470d0a1a0a')
+    expect(background.readUInt32BE(16)).toBe(660)
+    expect(background.readUInt32BE(20)).toBe(400)
+  })
+
   it('configures the Windows x64 NSIS installer', () => {
     expect(desktopPackage.build.win.target).toEqual([{ target: 'nsis', arch: ['x64'] }])
     expect(desktopPackage.build.nsis).toEqual({

apps/desktop/tests/packaging-config.spec.ts

@@ -1,4 +1,4 @@
 {
-  "sourceHash": "0cff6a0f19b48a2c0372aee63de7a176f5d499a92f2e6d297c5e456376f63283",
+  "sourceHash": "5e490fdbfda9e6666965a6c99496a2fc8f5e34ed8df8ab61ec9342ea5f19932c",
   "sourceFileCount": 411
 }