The previous hot-reload fix covered the running CLI process, but empty desktop sessions build their slash skill list through the server-side /api/skills path. If the server had already cached disabled plugin settings, /api/plugins/reload could still reload plugin state from stale settings and /api/skills stayed empty until a real chat spawned a fresh CLI.
Reset the server settings cache at the plugin reload boundary before clearing plugin caches. This keeps the desktop server, active CLI reload, and empty-session skills API aligned on enable-after-disable transitions.
Constraint: EmptySession uses /api/skills, not the active CLI slash-command cache
Rejected: Rely on starting a real CLI session to repopulate skills | delays visibility and makes empty-session slash commands stale
Confidence: high
Scope-risk: narrow
Directive: Plugin reload paths must invalidate settings before resolving enabledPlugins
Tested: bun test src/server/__tests__/skills.test.ts src/server/__tests__/plugins.test.ts
Tested: bun run check:server
Tested: cd desktop && bun run test --run src/pages/EmptySession.test.tsx src/stores/pluginStore.test.ts
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