IntelliJ Codex/MCP companion tool surface collapses during session; exact file-read tool disappears

[mightydanp]

Environment

• Project: /home/chris/Projects/Tech-Ascension-Workspace
• IntelliJ IDEA open with the project open
• Indexing: false
• Codex/IntelliJ MCP companion integration
• MCP server configured as idea_http_server / IntelliJ companion
• Shell intentionally disabled, so workflows depend on MCP file-read tools
• Expected read tool from config/tool allowlist: get_file_text_by_path

Symptoms

• The Codex-visible idea_http_server tool surface changes during the session and can collapse from a broad surface to a partial one.
• Observed visible tool counts across attempts: 2, 9, and 15.
• When collapsed, get_file_text_by_path is missing.
• Restarting IntelliJ temporarily restores a larger tool surface.
• Starting a new Codex chat without restarting IntelliJ does not restore the full tool surface.
• The IDE-side companion overview still reports broad categories:
  • editor/navigation
  • project/file
  • build/test
  • debug
  • VCS
  • diagnostics/processes
  • general tools

Expected behavior

• The Codex-visible MCP tool surface should stay aligned with the IDE-side companion registry.
• If IntelliJ’s companion registry refreshes dynamically, Codex should renegotiate and see the updated tool list without requiring an IntelliJ restart.
• get_file_text_by_path should remain available if it is still part of the supported surface, or the replacement exact-file-read tool should be clearly exposed and stable.

Actual behavior

• The IDE-side companion registry reports a broad tool set, but Codex only sees a partial subset.
• The visible tool surface appears to collapse or change during the same IntelliJ session.
• New Codex chats do not force the full tool list to reappear.
• The mismatch blocks workflows that require exact file reads, especially instruction-file maintenance in hidden dot folders such as .agents/skills/**/SKILL.md.

Evidence

• Project open in IntelliJ: /home/chris/Projects/Tech-Ascension-Workspace
• indexing: false
• Companion overview reports broad tool categories, including editor/navigation, project/file, build/test, debug, VCS, diagnostics, and general tools.
• Earlier IDE log evidence showed:
  • FeatureRegistry[Tool] - Added Tools: 127
  • ToolListChangedNotification
• Visible idea_http_server tool counts observed during the session: 2, 9, 15
• get_file_text_by_path was missing when the surface was collapsed
• Restarting IntelliJ temporarily restored a larger tool surface
• A new Codex chat without restarting IntelliJ did not restore the full tool surface

Reproduction steps

1. Open IntelliJ with /home/chris/Projects/Tech-Ascension-Workspace.
2. Confirm the project is open and indexing is false.
3. Observe the Codex-visible idea_http_server tool list.
4. Restart IntelliJ.
5. Observe that more tools appear temporarily.
6. Continue the session and start a new Codex chat without restarting IntelliJ.
7. Observe that the visible tool surface can collapse again.
8. Compare the IDE-side companion overview against the Codex-visible tool list.
9. Check whether get_file_text_by_path is present.

Workarounds tried

• Restarting IntelliJ
• Starting a new Codex chat without restarting IntelliJ
• Rechecking the companion overview after the collapse

Questions

1. How can ACP/MCP capability renegotiation be forced without restarting IntelliJ?
2. Is this a known issue with dynamic tool registry refresh or session reuse?
3. What logs are needed to diagnose why Codex only sees a partial tool set?
4. Was get_file_text_by_path renamed, gated, or removed in the current plugin build?
5. Is there a supported exact file-read tool that should replace get_file_text_by_path?