fix: resolve env-var placeholders in Codex/Gemini self-defined stdio MCP (closes #1266)

[edenfunf]

Summary

Self-defined stdio MCP servers declared in apm.yml had their env block written verbatim to ~/.codex/config.toml and .gemini/settings.json. All three placeholder syntaxes (${VAR}, ${env:VAR}, legacy <VAR>) ended up as literal strings, causing the MCP child process to fail authentication.

This PR resolves them at install time, matching the Copilot/Cursor pattern and consistent with the documented manifest-schema behaviour.

Root cause

1. Codex and Gemini's _raw_stdio branch assigned raw["env"] directly to config["env"], skipping the resolver entirely.
2. Even adapters that did call _resolve_environment_variables (Cursor) hit a latent gap: the legacy-mode branch only handled the registry list-of-dict shape, so the dict-shape input from self-defined stdio deps was iterated as keys, every key failed isinstance(env_var, dict), and the env block came out as {}.
3. Codex extends MCPClientAdapter directly (not CopilotClientAdapter), so the resolver wasn't even available on the class.

Fix

• Move _resolve_environment_variables, _resolve_env_variable, _resolve_variable_placeholders, the env-placeholder regex helpers, and the per-server placeholder state to MCPClientAdapter so every adapter shares one resolver contract.
• Add a legacy-mode dict-shape branch to _resolve_environment_variables (matches the fix in fix: preserve Claude stdio MCP env #1224 for Claude). Cursor's silent-drop latent bug dies as a byproduct.
• Rewrite Codex/Gemini's _raw_stdio branch to route env through the resolver and args through _resolve_variable_placeholders, with the same shape as the existing Cursor/Copilot branches.
• Centralise the prompt-suppression policy in a single _should_skip_env_prompts helper.

Production code is net ~0 lines (mostly relocation); tests add ~180 lines of regression coverage.

Related

• [BUG] Codex and Gemini adapters pass self-defined stdio env verbatim, skipping placeholder resolution #1266 — this issue
• [BUG] Claude .mcp.json drops env for self-defined stdio MCP servers #1222 — same defect class in the Claude adapter
• fix: preserve Claude stdio MCP env #1224 — Claude fix (independent; this PR carries the dict-shape branch so it does not depend on fix: preserve Claude stdio MCP env #1224 landing first)

Test plan

• Existing 258 adapter unit tests pass
• New regression tests: Codex (3), Gemini (3), Cursor (1, pins the latent bug), base-resolver dict-shape branch (3)
• End-to-end apm install -t codex,gemini,cursor with all three placeholder syntaxes in apm.yml; resolved values written to disk for legacy-mode adapters; Copilot translate-mode unchanged (placeholders kept as runtime substitution)
• ruff check + ruff format --check clean

[Copilot]

Pull request overview

This PR fixes placeholder resolution for self-defined stdio MCP servers declared in apm.yml, ensuring Codex and Gemini no longer write ${VAR} / ${env:VAR} / <VAR> placeholders verbatim into their generated config files. It also centralizes env/arg placeholder resolution logic so all adapters share the same behavior, and adds regression coverage for Codex/Gemini/Cursor plus the shared resolver.

Changes:

• Move env/arg placeholder resolution helpers into MCPClientAdapter so all client adapters share a single resolver contract.
• Update Codex and Gemini _raw_stdio formatting to route env through _resolve_environment_variables and args through _resolve_variable_placeholders.
• Add regression tests covering the fixed placeholder resolution behavior and the previously latent dict-shape env drop.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/apm_cli/adapters/client/base.py	Adds shared env/arg placeholder resolution and prompt-suppression policy to the base adapter.
src/apm_cli/adapters/client/copilot.py	Removes duplicated resolver helpers and imports shared helpers from the base adapter.
src/apm_cli/adapters/client/codex.py	Ensures self-defined stdio env/args flow through the shared resolver pipeline.
src/apm_cli/adapters/client/gemini.py	Ensures self-defined stdio env/args flow through the shared resolver pipeline.
tests/unit/test_copilot_adapter.py	Adds base-resolver regression tests for legacy-mode dict-shaped env blocks.
tests/unit/test_cursor_mcp.py	Adds a regression test proving Cursor no longer drops dict-shaped stdio env blocks.
tests/unit/test_gemini_mcp.py	Adds Gemini regression tests for resolving all placeholder syntaxes (env + args).
tests/test_codex_empty_string_and_defaults.py	Adds Codex regression tests for resolving all placeholder syntaxes (env + args).