[Bug] Desktop app does not inherit user env vars into Bash subprocess (BASH_DEFAULT_TIMEOUT_MS etc.)

Problem

ZCode desktop (Windows 11 Pro, v3.3.6) does not pass user environment variables into Bash subprocesses spawned by the Bash tool. Only ZCODE_* variables explicitly injected by ZCode are visible. This breaks documented Claude Code env vars like BASH_DEFAULT_TIMEOUT_MS, CLAUDE_BASH_MAINTAIN_PROJECT_WORKING_DIR, API_TIMEOUT_MS, etc.

This appears to be the same root cause as anthropics/claude-code#42203 ("Desktop app ignores env.PATH from settings.json — sandbox overrides").

Reproduction

1. Set a user env var on Windows:

   setx BASH_DEFAULT_TIMEOUT_MS "300000"
   setx ZCODE_TEST_ENV_VAR "hello-from-setx"
   

2. Restart ZCode desktop.
3. Open a chat, ask the agent: "print all env vars containing ZCODE_TEST or BASH_DEFAULT".
4. The agent runs env | grep ... via Bash tool.

Expected

Both ZCODE_TEST_ENV_VAR=hello-from-setx and BASH_DEFAULT_TIMEOUT_MS=300000 should be visible in the subprocess.

Actual

ZCODE_APP_VERSION=3.3.6
ZCODE_RUNTIME_ENV=production
ZCODE_WINDOWS_APP_INSTALL_DIR=...
ZCODE_RG_BINARY=...
ZCODE_PROCESS_LABEL=local-1
ZCODE_BASE_URL=https://zcode.z.ai
ZCODE_ENV=production

No BASH_DEFAULT_TIMEOUT_MS, no ZCODE_TEST_ENV_VAR, no user-set vars. Only ZCode-injected ones appear.

Also tried: setting an env block in ~/.zcode/cli/config.json:

{ "env": { "BASH_DEFAULT_TIMEOUT_MS": "300000" } }

Same result — the var is not visible in subprocess.

Note: env field inside MCP servers DOES work

For comparison, the env field inside an MCP server config is honored correctly:

{
  "mcp": { "servers": { "excel": {
    "env": { "EXCEL_MCP_PAGING_CELLS_LIMIT": "4000" }
  } } }
}

This works — the var reaches the MCP server process. The issue is specifically with the Bash/Read/Edit/Write built-in tools.

Impact

• Documented Claude Code env vars (BASH_DEFAULT_TIMEOUT_MS, API_TIMEOUT_MS, CLAUDE_BASH_MAINTAIN_PROJECT_WORKING_DIR, etc.) are non-functional in ZCode desktop.
• Users relying on these for long-running test suites / deploy scripts get silent breakage with default 2-min timeout.

Environment

• ZCode 3.3.6, Windows 11 Pro (10.0.26200).
• GLM-5.2 via Z.ai Coding Plan (Max).
• PowerShell setx confirmed the vars were stored in User registry.

Related

• anthropics/claude-code#42203 — same issue in upstream Claude Code.
• The env field for MCP servers works (so the parser exists), it's the Bash tool subprocess that is isolated.

Proposal

Either:

1. Honor the env block in ~/.zcode/cli/config.json for built-in tool subprocesses (matching Claude Code docs).
2. Or inherit user-level environment variables on desktop launch.
3. Or document clearly that these env vars are CLI-only and provide a ZCode-specific way to set them.

Thanks — happy to provide more diagnostics if useful.

Start by reproducing the behavior on Windows with a user variable and the env block in ~/.zcode/cli/config.json, then compare the built-in Bash/Read/Edit/Write tools with the working MCP server env handling. Done means user-level variables or the documented config env values reach built-in tool subprocesses, with the intended behavior clarified among the listed proposals.