Unclear Whether the note about a skipped file is shown on screen or only written to the debug log is not settled.
What
Instruction files are files such as CLAUDE.md, CLAUDE.local.md, AGENTS.md and rules files that Claude Code loads to learn about your project. When file reads are restricted, or blockReadsOutsideWorkingDirectories is set, Claude Code now checks each one before loading it:
- A file covered by a Read deny rule, or one that resolves to a location outside your working folders, for example through a symbolic link (a shortcut to another place), is skipped. The log records why, starting with "Instruction file not loaded".
- Claude Code also times how long the auto-memory index takes to load.
- For hooks modules,
$.fs.ancestorsnow accepts held and session options and treatsAGENTS.mdand.claude/AGENTS.mdspecially, applying the same outside-the-folder check. - When a plugin withholds the result of a call, the error now says whether the call had "started" or "ran" before the plugin withheld its result, instead of just
$.<name>: <reason>.
Why
A CLAUDE.md that is symlinked from elsewhere or covered by a deny rule can now silently stop loading when reads are restricted. If Claude seems to ignore your instructions, check the log for "Instruction file not loaded". Plugin authors using hooks modules see the new AGENTS.md handling and clearer withheld-result errors.
The entry above is what we published on the day. These lines were added later, as Anthropic's own pages caught up, and they sit beside the original rather than replacing it.
While [`permissions.blockReadsOutsideWorkingDirectories`](/docs/en/settings-reference#permissions-blockreadsoutsideworkingdirectories) is off, file reads other than [reads from network paths](/docs/en/permissions#network-paths) run without…permission-modes see the edit
The network and filesystem sandboxes apply on macOS, and on Linux devices and [SSH hosts](/docs/third-party/claude-desktop/ssh-remote-sessions#managed-configuration-on-the-remote-host) with Claude Code's [sandbox dependencies](https://code…third-party/claude-desktop/code see the edit
Whether the note about a skipped file is shown on screen or only written to the debug log is not settled.
A small documentation edit on Code in Claude Desktop on 3P touched a line naming blockReadsOutsideWorkingDirectories after this was…
Fixed a project CLAUDE.md, rule or AGENTS.md symlinked outside the working directories loading under…