[Feature Request] Plan mode should support plan files outside ~/.claude/plans directory

Bug Description
New plan mode (is this the V2 that I saw env vars for?) can ONLY use plan files in ~/.claude/plans, which breaks many workflows that use plan files in other places.

slightly more detail

The new plan mode is a step in the right direction. I started writing context to files for managing cross-session work waaaay back in june, so I'm glad to see it formalized. BUT

BUT the new plan mode breaks a few things. I tend to like to version control my plan files - it makes it easier to review the code and run other LLMs or even other claude code sessions to check the work product. A bit like antigravity before antigravity.

The new plan mode seems to FORCE using the plans in ~/.claude/plans, even when I explicitly ask it to use sentry-architecture-redesign-plan.md or something like it.

When I'm lucky after compaction it will remember to also read my plan file:

  ⎿  Referenced file copilot_notes/sentry-architecture-redesign-plan.md
  ⎿  Read ../../../.claude/plans/abstract-fluttering-unicorn.md (145 lines)

But this is very brittle. When planning, it's also VERY confusing! Which plan is it presenting with ExitPlanMode? Is it abstract-fluttering-unicorn.md or sentry-architecture-redesign-plan.md? What's the actual difference?

Then there are... other sillynesses... like, asking claude to edit the plan files in ~/.claude, when outside of plan mode, triggers the permissions request prompt because it's editing a file in .claude! If I ask it to make a bunch of changes to the file... a bunch of requests, because .claude directories are never allowed to "always accept edits" for what I presume are obvious security reasons. Oopsies.

@ed-irl has shared a closely related bug report here:
https://github.com/anthropics/claude-code/issues/12619

I think this is clearly related, here in @jgwill's report:
https://github.com/anthropics/claude-code/issues/12499

I think this is a parallel problem, as I've seen the new permissions for plan mode (enforcing read only more aggressively?) break writes by the Plan subagent when I ask it to edit my own plan files (e.g. sentry-architecture-redesign-plan.md), in @alexn-tinwell's issue:
https://github.com/anthropics/claude-code/issues/12434

I _very_ vaguely suspect this is related: https://github.com/anthropics/claude-code/issues/12595

For what it's worth, I think the comments in this issue are incorrect:
https://github.com/anthropics/claude-code/issues/12366

I almost _always_ want my plan files to be as thorough as possible. Getting things done faster is not super valuable to me if they're not done correctly... I can do things arbitrarily fast if they don't have to be correct!

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.0.55
• Feedback ID: accd68fd-35be-499f-944b-532b6c25038a

Errors

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