What version of Codex CLI is running?
codex-cli 0.104.0
What subscription do you have?
Logged in using ChatGPT (plan tier unknown).
Which model were you using?
gpt-5.3-codex
What platform is your computer?
macOS v26.3
What terminal emulator and version are you using (if applicable)?
Codex Desktop app (internal terminal context). In-command env shows TERM=dumb and empty TERM_PROGRAM.
What issue are you seeing?
Project-scoped MCP config is ignored for this thread/workspace.
In /Users/prb/sablier/new-ui, .codex/config.toml contains a valid Serena MCP server entry:
[mcp_servers.serena]
command = "uvx"
args = ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server", "--context", "codex", "--project-from-cwd"]
But inside the Codex Desktop thread runtime, Serena is missing:
- available MCP resources/templates are empty for Serena tools
- Serena tools (
find_symbol, rename_symbol, etc.) are not exposed
codex mcp list only shows servers from ~/.codex/config.tomlcodex mcp get serena returns: No MCP server named 'serena' found.
The Serena command itself works when run manually, so startup command/config appears valid.
What steps can reproduce the bug?
- In a project, configure Serena only in project-local
.codex/config.toml (not in ~/.codex/config.toml).
- Open that project in Codex Desktop.
- Start a thread and inspect MCP availability.
- Run
codex mcp list and codex mcp get serena from the same workspace.
- Observe that only user-level servers are loaded and Serena is absent.
- Run Serena manually:
uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context codex --project-from-cwd
- Observe manual startup succeeds.
Thread ID: 019c9ffc-da8e-7500-8768-c516825ce9ce
What is the expected behavior?
Project-scoped .codex/config.toml should be merged into runtime MCP config (for trusted projects), so Serena should be available in the Desktop thread/toolset.
Additional information
Possibly related to MCP visibility inconsistency issues in Desktop (for example #10499), but this repro is specifically about project-local config not being loaded while user-global config is.
What version of Codex CLI is running?
codex-cli 0.104.0What subscription do you have?
Logged in using ChatGPT (plan tier unknown).
Which model were you using?
gpt-5.3-codexWhat platform is your computer?
macOS v26.3
What terminal emulator and version are you using (if applicable)?
Codex Desktop app (internal terminal context). In-command env shows
TERM=dumband emptyTERM_PROGRAM.What issue are you seeing?
Project-scoped MCP config is ignored for this thread/workspace.
In
/Users/prb/sablier/new-ui,.codex/config.tomlcontains a valid Serena MCP server entry:[mcp_servers.serena]command = "uvx"args = ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server", "--context", "codex", "--project-from-cwd"]But inside the Codex Desktop thread runtime, Serena is missing:
find_symbol,rename_symbol, etc.) are not exposedcodex mcp listonly shows servers from~/.codex/config.tomlcodex mcp get serenareturns:No MCP server named 'serena' found.The Serena command itself works when run manually, so startup command/config appears valid.
What steps can reproduce the bug?
.codex/config.toml(not in~/.codex/config.toml).codex mcp listandcodex mcp get serenafrom the same workspace.uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context codex --project-from-cwdThread ID:
019c9ffc-da8e-7500-8768-c516825ce9ceWhat is the expected behavior?
Project-scoped
.codex/config.tomlshould be merged into runtime MCP config (for trusted projects), so Serena should be available in the Desktop thread/toolset.Additional information
Possibly related to MCP visibility inconsistency issues in Desktop (for example #10499), but this repro is specifically about project-local config not being loaded while user-global config is.