I have the same problem. If my sandbox includes `denyRead: ["~"]`, claude consistently tries to do things inside my home directory. For example, every time I start claude I tell it to "run pwd".
And every time it says this:
Bash(pwd)
⎿ /home/<username>
⎿ Shell cwd was reset to /home/<username>/Projects/<current-working-dir>
This breaks a bunch of features in inconsistent ways (e.g., `git status` sometimes works and sometimes doesn't).
There are issues reporting this problem to Anthropic but they are all closed with no helpful comments: