Add scenarios for testing bootstrap loading order.
Add scenarios for testing bootstrap loading order.

Added scenarios:
- `Install a package that overrides a command bundled in source`
- `Install a package that overrides a bundled PHAR command`

Both scenarios are tagged with `@bootstrap`.

See #3850

aaemnnosttv/wp-cli,miya0001/wp-cli,gitlost/wp-cli,GaryJones/wp-cli,aaemnnosttv/wp-cli,miya0001/wp-cli,aaemnnosttv/wp-cli,GaryJones/wp-cli,trepmal/wp-cli,rodrigoprimo/wp-cli,rodrigoprimo/wp-cli,trepmal/wp-cli,trepmal/wp-cli,miya0001/wp-cli,rodrigoprimo/wp-cli,2ndkauboy/wp-cli,gitlost/wp-cli,GaryJones/wp-cli,gitlost/wp-cli,2ndkauboy/wp-cli,2ndkauboy/wp-cli