Ninja: Remove shell workaround from compilation database

Commit 1528113bdf (instrumentation: Prevent inherited process metrics in
chained commands, 2026-09-14) added an extra command to successfully
track process metrics for instrumentation, working around shell exec
optimizations . However, this workaround gets exported into
`compile_commands.json` when using the Ninja generator, which breaks
some tools that consume the database.

Append this no-op command only when generating the actual build files.