[BUG] --allowedTools no working reliably

[TomDigitalDavid]

Environment

• Platform (select one):
  • Anthropic API
  • AWS Bedrock
  • Google Vertex AI
  • Other:
• Claude CLI version: 0.2.49
• Operating System: Windows (Windows Server 2022 Datacenter)
• Terminal: WSL2

Bug Description

I am trying to run Claude Code from a script using a command like claude -p "test the application and fix any errors you encounter" --allowedTools "Bash(dotnet:*)" Edit.
Claude Code will always reply that it needs permissions for the Edit tool, when it encounters an error. When prompting Claude Code to simply edit a file with the same --allowedTools specification it can edit files.

Steps to Reproduce

1. Open WSL terminal in a .NET project
2. Prompt it something like claude -p "test the application and fix any errors you encounter" --allowedTools "Bash(dotnet:*)" Edit
3. It runs the tests and then you get a reply that it needs permissions to edit files (if it encounters errors)
4. Prompt something like claude -p "Check which files you have access to and give me list of the files' names. Then write 'test' at the end of README.md. If you require permissions stop your task and reply with a message explaining what permissions you need." --allowedTools Edit
5. Result: Claude Code can execute Bash (ls) and edit the file.

Expected Behavior

I would expect Claude Code to work the same in interactive mode and non-interactive mode, i.e. either use the allowedTools as defined in the project's claude config or correctly apply the --allowedTools flag with its parameters.
When using --allowedTools I expect Claude Code to use all tools defined with the command.

Actual Behavior

Claude Code cannot use all tools that were defined with --allowedTools

Additional Context

I'm running Claude Code in WSL on a virtual machine.
I played around with different prompts and different --allowedTools configurations. I could not find an explanation as to why this happens. When giving Claude Code a task like claude -p "Write 'hello' to README.md" --allowedTools Edit it worked. The same when I used a prompt that required it to run a bash command like "ls" and then edit a file.
I also added more allowed tools to the prompt and it still worked. Somehow, it failed once the prompt got a bit more complex, i.e. run "dotnet test" and then, if there are error during the build, editing files.

[maschwenk]

Can repro this as well, and can also confirm that claude -p "Write 'hello' to README.md" --allowedTools Edit DOES seem to work.

Reproing on a Mac talking to Bedrock. 0.2.49 (Claude Code)

[maschwenk]

Maybe it has nothing to do with the prompt, but more that --allowedTools is not accepting a list properly? Or it's not working with --print mode specifically?

I tried providing the arguments a few different ways like --allowedTools X --allowedTools Y and still didn't work.

[maschwenk]

Ok I figured it out. The docs are wrong.

export ANTHROPIC_API_KEY=sk_...
claude -p "update the README with the latest changes" --allowedTools "Bash(git diff:*)" "Bash(git log:*)" Edit

https://docs.anthropic.com/en/docs/agents-and-tools/claude-code/overview#automate-ci-and-infra-workflows

but actually if you look at claude --help you can see the correct format is:

--allowedTools <tools> Comma-separated list of tool names to allow (e.g. "Bash(git*),Edit,Replace")

e.g.

claude -p "update the README with the latest changes" --allowedTools "Bash(git diff:*),Bash(git log:*),Edit"

[bcherny]

Fix incoming

[TomDigitalDavid]

@maschwenk You are right. I tested my workflow with --allowedTools "Bash(dotnet:*),[...some other tools...],Edit" and it worked fine. Thanks for your help!

@bcherny Thanks for your quick response!

[maschwenk]

@bcherny Awesome! Just also noting using --print mode in CI makes it super hard to understand when permissions are failing. It'll say "I had permissions issues doing X" but it doesn't really call out what command it ran so it's really hard to build the --allowedTools list. I've tried adding things like

As you work on this, please print any output to the file and well as a summary of each command you execute to ./.git/claude-code-output.txt with a timestamp.

or

if you run into any issues please tell me which command failed and why

but never works

[bcherny]

Fixed in the latest!

[bcherny]

@maschwenk mind commenting on #365?

[maschwenk]

@bcherny For sure. Can you clarify exactly what you changed here though? Did you update the docs to match the code? Or change the code to match the docs?

[ijohnson-coursera]

@bcherny This is still an issue in 0.2.53. Still getting permission issues when I run Claude Code with the following. It seems to work most of the time, but about 20% of the time it will say it doesn't have access to write or commit/push.

CLAUDE_CODE_USE_BEDROCK=1 DISABLE_PROMPT_CACHING=1 claude -p "/init" --allowedTools "Bash(git diff:*),Bash(git status:*),Bash(git log:*),Bash(git show:*),Bash(git blame:*),Bash(git add:*),Bash(git commit:*),Bash(git checkout:*),Bash(git branch:*),Bash(git push:*),Bash(gh pr:*),Bash(gh auth:*),Bash(./gradlew build:*),Bash(./gradlew clean build:*),Bash(./gradlew test:*),Bash(./gradlew checkstyleMain:*),Bash(./gradlew idea:*),Bash(./gradlew eclipse:*),Bash(./gradlew generateProto:*),Edit,Write"

[ijohnson-coursera]

Seems like doing "--allowedTools Bash Edit Replace" and not specifying the bash command works