[Bug]: t3 update / t3 service install re-render the service unit and drop every user environment variable, including the documented Bitbucket credentials #12626

Before submitting

• I searched existing issues and did not find a duplicate.
• I included enough detail to reproduce or investigate the problem.

Area

apps/server

Steps to reproduce

1. On macOS, run t3 service install.
2. Follow docs/user/source-control.md for Bitbucket: add T3CODE_BITBUCKET_EMAIL and T3CODE_BITBUCKET_API_TOKEN to the service's environment. The only place launchd takes environment for this job is EnvironmentVariables in ~/Library/LaunchAgents/com.t3tools.t3code.service.plist, so add them there and launchctl bootout / bootstrap.
3. Confirm Settings → Source Control shows Bitbucket authenticated.
4. Run t3 update (or run t3 service install again to "repair" the service, as docs/user/background-service.md suggests).

Expected behavior

Environment the user added to the service survives an update or reinstall, or there is a documented place to put service environment that t3 does not overwrite.

Actual behavior

The plist is re-rendered from a fixed template and the user's entries are gone. Bitbucket reverts to "Available. Set T3CODE_BITBUCKET_EMAIL and T3CODE_BITBUCKET_API_TOKEN on the server". The same happens to T3CODE_PORT / T3CODE_HOST pins, so a service pinned off the default port silently moves back to port scanning after an update.

Mechanics:

• renderBootServicePlist (apps/server/src/cloud/bootService.ts ~L134) emits exactly PATH, T3CODE_HOME, and T3_BOOT_SERVICE_UNIT. renderBootServiceUnit does the same for systemd.
• install() unconditionally runs writeDurably(unitPath, manager.render(plan)) (~L885). The only value read back from an existing unit is T3CODE_HOME via bootServiceBaseDirOf (~L64).
• t3 update calls install() on every version switch (apps/server/src/cli/update.ts ~L559, comment: "The unit is rewritten either way").
• On Linux a systemctl --user edit drop-in would survive this. launchd has no override mechanism, so on macOS there is nowhere to put service environment that t3 will not delete.
• docs/user/source-control.md tells Bitbucket users to export the variables "in the server's environment" and never mentions the background service; docs/user/background-service.md never mentions environment. Bitbucket is the only provider that needs environment, because it has no CLI to hold credentials.

Suggested fixes (any one would do):

1. Preserve unknown EnvironmentVariables / Environment= entries when re-rendering an existing unit.
2. Have the launcher read an optional env file (e.g. $T3CODE_HOME/service.env) and document it.
3. Store Bitbucket credentials in the server's existing secrets store, settable from Settings → Source Control, so no environment is needed.

Impact

Blocks a workflow (Bitbucket source control cannot be kept working on a macOS background service across updates)

Version or commit

0.0.42 → 0.0.43-nightly.20260919.1962

Environment

macOS 26.6 (Darwin 25.6.0), arm64, background service via launchd

Logs or stack traces

# after `t3 update`, the regenerated plist EnvironmentVariables dict contains only:
PATH, T3CODE_HOME, T3_BOOT_SERVICE_UNIT

Workaround

Keep the variables out of t3's plist: a separate user LaunchAgent that runs launchctl setenv T3CODE_BITBUCKET_EMAIL … ; launchctl setenv T3CODE_BITBUCKET_API_TOKEN … ; launchctl kickstart -k gui/$UID/com.t3tools.t3code.service at login. The service inherits the domain environment and t3 never touches that file.