Anyone else hitting permission prompts on every MEMORY/WORK write?

[javierburongarcia]

PAI stores session artifacts (PRDs, work logs, memory) under ~/.claude/MEMORY/WORK/. Claude Code hardcodes .claude/ as a protected directory with a separate "config-write" gate that fires on every write — even with all of these set:

• --dangerously-skip-permissions CLI flag
• permissions.defaultMode: "bypassPermissions" in settings.json
• Write in permissions.allow

The result: every PRD creation triggers "Do you want to create PRD.md?" with the Yes/No prompt. Every session, multiple times.

What I've confirmed

• The .claude/ gate is separate from the general permission system — the bypass flag doesn't override it
• Only .claude/commands, .claude/agents, .claude/skills are exempt
• Symlinks from inside .claude/ to outside paths still trigger it (path string check)
• Writes to paths outside .claude/ work perfectly with the bypass flag

Workarounds I'm considering

1. Moving MEMORY/WORK/ to a path outside .claude/ (e.g., ~/data/work/) and updating all Algorithm/hook references
2. Filing an upstream Claude Code issue requesting .claude/MEMORY/ as an additional exemption

Questions for the community

• Is anyone else running into this with their PAI setup?
• Has anyone already moved session storage outside .claude/? Any gotchas?

Environment: Claude Code 2.1.81, PAI 4.0.3, Linux VM

[javierburongarcia]

Seems to be a bug introduced by recent claude code versions, I am staying on 2.1.77 and seems to be working

[brycemagera]

I added the MEMORY directory path to "additionalDirectories" in settings.json and it fixed this for me. On my phone right now, but I can send an exact snippet later.

[virtualian]

additionalDirectories did not work for me: see anthropics/claude-code#29013 (comment) for details.

Reference: anthropics/claude-code#29013.

[brycemagera]

Submitted a PR here to fix it!

[javierburongarcia]

Thanks, will have a look at that!