How to handle doctrine migrations in bundles
I ended up creating a command that will copy all migration files from predefined directories in bundles to the default location and then executing doctrine:migrations:migrate from within the command.
For a complex deployment, I used phing. He easily integrate with the Symfony console. But in the end I use of a simple code on the Synfony console.Composer can easily call Symfony app commands as "post-install-cmd"
I don't think "composer loaded bundles" is the issue here. For instance, you could have several bundles in src/ (part of the app or submoduled) and have the exact same problem. The issue is having multiple entity managers and databases for your different bundles. Where they actually reside is trivial.
Anyway, I'm having the exact same problem. After some searching, I discovered there is actually an open pull request to fix this: https://github.com/doctrine/DoctrineMigrationsBundle/pull/46
I'm hoping it gets fixed soon!