bug: main agent does not load .pi/APPEND_SYSTEM.md in isolated runtime sessions

[marcinkardas]

Operating system(s)

• Windows
• macOS
• Linux

What happened?

New Howcode main-agent sessions loaded AGENTS.md project context, but did not apply .pi/APPEND_SYSTEM.md. The project was trusted and the file existed, so APPEND_SYSTEM instructions should have been appended to the system prompt.

Suggested fix

Howcode isolated runtime creates its own DefaultResourceLoader in desktop/runtime/isolated-settings-manager.ts. In that path, AGENTS.md is loaded normally, but APPEND_SYSTEM.md is not forwarded when using the custom isolated setup.

Fix:

• In createIsolatedRuntimeResourceLoader, detect trusted project .pi/APPEND_SYSTEM.md.
• Pass it to DefaultResourceLoader via appendSystemPrompt.
• Keep global APPEND_SYSTEM.md fallback.
• Do not include project APPEND_SYSTEM.md when projectTrusted is false.
• Add tests in desktop/runtime/isolated-settings-manager.test.ts for trusted and untrusted project APPEND_SYSTEM.md.

Expected code area:

• desktop/runtime/isolated-settings-manager.ts
• desktop/runtime/isolated-settings-manager.test.ts

Steps to reproduce

1. Open a trusted project containing .pi/APPEND_SYSTEM.md and AGENTS.md.
2. Start a new main-agent session in Howcode.
3. Ask the agent about loaded project instructions or use a marker instruction from APPEND_SYSTEM.md.
4. Observe that AGENTS.md is present, but APPEND_SYSTEM.md behavior is missing.

Agent implementation prompt

Investigate why Howcode main-agent isolated runtime sessions load AGENTS.md but do not apply .pi/APPEND_SYSTEM.md. Inspect the runtime resource loader setup and project trust path. Implement the smallest safe fix so trusted project APPEND_SYSTEM.md is passed into DefaultResourceLoader for isolated runtime sessions, while untrusted project APPEND_SYSTEM.md remains excluded. Add or update tests covering trusted and untrusted APPEND_SYSTEM loading.

App version or commit

0.1.66-dev