Remove exception for bootloader.

| Q             | A
| ------------- | ---
| Bug fix?      | no
| New feature?  | no
| BC breaks?    | no
| Deprecations? | no
| Tests pass?   | yes
| Fixed tickets | -
| Refs tickets  | #1424
| License       | MIT
| Doc PR        | -

Tricky situation to solve. If a module is uninstalled and the files
removed the autoloader table needs to be updated. But the Extensions
module currently auto-populates on regenerate. Maybe we need a #
REMOVED state flag? Something to consider in the workflow.