Partial rebuild should treat moved modules correctly

[kilian]

Following suggestions by BC, some modifications in the Makefiles should help, minimizing the impact of further invocations of #499.

[kilian]

Refactored the corresponding section in all Makefiles, where applicable:

• Modules is now contained in the BUILT_SOURCES set.
• This file is only (re)written if there is an actual change of content.
• The target still depends only on Makefile as a prerequisite, since the Makefile necessarily changes when we move a module.

I hope this settles the issue (r6570).