regression on update from 0.39.0 to 0.39.1

[oprudkyi]

What happened?

after update it crashes (github action for review pr) with

Gemini CLI is not running in a trusted directory. To proceed, either use `--skip-trust`, set the `GEMINI_CLI_TRUST_WORKSPACE=true` environment variable, or trust this directory in interactive mode. For more details, see https://geminicli.com/docs/cli/trusted-folders/#headless-and-automated-environments

and if GEMINI_CLI_TRUST_WORKSPACE=true set, then it starts but can't find any mcp (github) with errors in logs like

Tool \"github:pull_request_read.get\" not found. Did you mean \"run_shell_command\"?

forcing back to 0.39.0 fixes issue

What did you expect to happen?

no errors

Client information

Client Information

Run gemini to enter the interactive CLI, then run the /about command.

> /about
# paste output here

Login information

No response

Anything else we need to know?

No response

[shyamHugo]

Facing the same issue in GitHub Actions CI

Environment:

Gemini CLI: @google/gemini-cli@latest (installed via npm)
GitHub MCP Server: ghcr.io/github/github-mcp-server:v1.0.3
Action: google-github-actions/run-gemini-cli@v0
Runner: ubuntu-latest
Symptoms:

All GitHub MCP tools fail with Tool not found the MCP server appears to register zero tools. This is confirmed in the debug tool stats where every github:* tool shows durationMs: 0 (Docker invoked but never executed). Simultaneously, run_shell_command is denied by policy even with GEMINI_CLI_TRUST_WORKSPACE: 'true' set and tools explicitly allowed via tools.core in settings.

Full STDERR:

Warning: 256-color support not detected.
YOLO mode is enabled. All tool calls will be automatically approved.
Error executing tool run_shell_command: Tool execution denied by policy.
Error executing tool github:pull_request_read: Tool "github:pull_request_read" not found. Did you mean "run_shell_command"?
Error executing tool github:pull_request_read: Tool "github:pull_request_read" not found. Did you mean "run_shell_command"?
Error executing tool github:pull_request_read: Tool "github:pull_request_read" not found. Did you mean "run_shell_command"?
Error executing tool github:get_pull_request: Tool "github:get_pull_request" not found. Did you mean "run_shell_command"?
Error executing tool github:get_pull_request_files: Tool "github:get_pull_request_files" not found. Did you mean "run_shell_command"?
Error executing tool github:get_pull_request_diff: Tool "github:get_pull_request_diff" not found. Did you mean "run_shell_command"?
Error executing tool run_shell_command: Tool execution denied by policy.
Error executing tool github:list_pull_requests: Tool "github:list_pull_requests" not found. Did you mean "run_shell_command"?
...
Error executing tool github:add_comment_to_pending_review: Tool "github:add_comment_to_pending_review" not found. Did you mean "run_shell_command"?
Error executing tool run_shell_command: Tool execution denied by policy.

What was tried (none resolved it):

Upgraded GitHub MCP Server from v1.0.2 → v1.0.3 (v1.0.2 had a known lockdown bug where github-actions[bot] wasn't trusted, v1.0.3 was supposed to fix this, but the symptom persists)
Set GEMINI_CLI_TRUST_WORKSPACE: 'true'
Explicitly allowlisted tools via tools.core in settings JSON
Used includeTools in MCP server settings
Tried both pull_request_read (v1.0.x consolidated format) and legacy tool names like get_pull_request
The model burns all session turns (maxSessionTurns: 50) attempting different tool name variants and terminates with FatalTurnLimitedError.

[onthebed]

Looking into the 0.39.0 → 0.39.1 regression path — I want to narrow down which command or model flow changed between those releases and reproduce it against the current CLI behavior.

[rsamborski]

I am observing the same issue:

[ehedlund]

The Gemini Review GitHub Action was updated in google-github-actions/run-gemini-cli#512. For more information on the new GEMINI_CLI_TRUST_WORKSPACE environment variable, see this advisory: GHSA-wpqr-6v78-jr5g. For guidance on how to update your workflows, see https://github.com/google-github-actions/run-gemini-cli/blob/main/docs/trust-guidance.md. Thanks!

[oprudkyi]

@ehedlund fix doesn't help

I have updated action to latest , added GEMINI_CLI_TRUST_WORKSPACE: true and again anything doesn't work.
as far as I see, the problem is the GEMINI_CLI_TRUST_WORKSPACE doesn't work correctly under cli call - doesn't add mcp, plugins and so on

[oprudkyi]

I didn't find a way to make it work with versions above 0.39.1 (mcp server doesn't register at all )
tried with

              "mcp": {
                "allow": [
                  "github"
                ]
              },

as well with tools.core.

so in the end replaced github mcp with native gh calls (like claude uses) and now everything works for me