[codex] Fix ctx_shell MCP command hangs

[xsploit]

Summary

• Prevent ctx_shell child processes from inheriting MCP stdio, which can block commands like Git inside MCP sessions.
• Disable Git prompts/pagers for shell execution so non-interactive calls return deterministically.
• Add a bounded command timeout plus regression tests for stdin closure and git --version.

Root cause

The MCP server uses stdin for JSON-RPC. Commands launched by ctx_shell inherited that stdin, so interactive or stdin-aware tools could block on the protocol stream instead of receiving EOF.

Validation

• cargo test --locked execute_command -- --nocapture
• cargo test --locked git_version_returns -- --nocapture
• git diff --check
• Manual MCP smoke: ctx_shell returned git --version and git status --short --branch immediately after reinstalling the patched binary.

[yvgude]

Thank you @xsploit for this excellent contribution! 🙌

The core fixes from this PR have been manually merged into v3.2.9 with the following additions:

What was adopted from your PR:

• stdin(Stdio::null()) — the critical fix preventing JSON-RPC pipe inheritance
• GIT_TERMINAL_PROMPT=0, GIT_PAGER=cat, PAGER=cat env vars
• Bounded command timeout with try_wait polling loop (120s default, configurable via LEAN_CTX_SHELL_TIMEOUT_MS)
• mpsc::channel pattern with recv_timeout for reader threads
• Both regression tests (execute_command_closes_stdin, git_version_returns_when_git_is_available)

Additional change on top of your PR:

• Replaced String::from_utf8_lossy with our new decode_output() function to fix UTF-8 corruption on Windows PowerShell (Issue bug: UTF-8 text is corrupted when using lean-ctx -c with Get-Content on Windows (PowerShell) #131)

Released in v3.2.9. You're credited in the CHANGELOG. Thanks for the thorough analysis and clean PR!

[yvgude]

Merged manually in v3.2.9. See comment above for details.