When using the shell executor, file variables that reference other
file variables (e.g., MY_FILE_VAR: $FILE_TEST) were incorrectly
getting a $PWD/ prefix, resulting in paths like:

$PWD/$FILE_TEST

This caused "No such file or directory" errors because the shell would
not expand the nested variable reference correctly.

The root cause was that the shell executor was using relative paths for
BuildDir (e.g., "builds/...") instead of absolute paths. This caused the
following chain of issues:

1. TmpProjectDir() returns a relative path
2. When creating file variables, TmpFile() -> Absolute() prepends
   $PWD/ to relative paths
3. File variables get paths like $PWD/builds/.../FILE_TEST
4. When MY_FILE_VAR: $FILE_TEST is processed, the literal string
   $FILE_TEST doesn't match the temp file check
5. It also goes through Absolute() and becomes $PWD/$FILE_TEST

The fix ensures DefaultBuildsDir and DefaultCacheDir are converted
to absolute paths during the Prepare() phase by joining them with
the current working directory if they are relative.

This makes the shell executor behavior consistent with the Docker
executor, which already uses absolute paths.

This was a regression introduced by
!5912.

Relates to #39124

Changelog: fixed