[BUG] Claude Code loses track of working directory, wastes time with failing calls and pwd: add better tooling

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Claude code often loses track of the current working directory.

In one step it changes directory with cd DIRNAME and then in the next bash call it wrongly assumes it's back in the root dir.

What Should Happen?

Claude code should never be wrong about the working directory it's in.

Somehow you don't add the current working directory properly to context. It shouldn't be hard to do this?

Error Messages/Logs

⏺ Now let me regenerate the Gradle lock file with the new Spring Boot 4.0 dependencies.

⏺ Bash(cd backend && rm gradle.lockfile && ./gradlew dependencies --write-locks) timeout: 3m 0s
  ⎿  Starting a Gradle Daemon (subsequent builds will be faster)

     > Task :dependencies
     … +452 lines (ctrl+o to expand)

⏺ Excellent! The lock file has been regenerated successfully. I can see that:
  - Spring Boot 4.0.0 is active
  - Spring Framework 7.0.1 is being used
  - Jackson 2 compatibility is working (using com.fasterxml.jackson 2.20.1)
  - Exposed 0.61.0 is unchanged

  Now let's attempt to build the project.
⏺ Bash(cd backend && ./gradlew clean build --console=plain 2>&1 | head -300) timeout: 5m 0s
  ⎿  Error: Exit code 1
     (eval):cd:1: no such file or directory: backend

⏺ Bash(pwd && ls -la | head -20)
  ⎿  /Users/cr/code/loculus/backend
     total 208
     drwxr-xr-x@ 29 cr  staff    928 Dec 17 12:58 .
     … +18 lines (ctrl+o to expand)

⏺ I'm already in the backend directory. Let me run the build.

⏺ Bash(./gradlew clean build --console=plain 2>&1 | head -300) timeout: 5m 0s
  ⎿  Running…
     ctrl+b to run in background

Steps to Reproduce

Not sure it's easy to reproduce.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

v2.0.71

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_