Yann,
If you have the influence, try to encourage your development manager to change their way of thinking and building applications. In all shops I've worked in or heard of, each major PL/SQL object (trigger, package, view) is contained within its own file. The file is named for the object within it. This gives you much finer-grained control over the source code for that object. Source code control is easier because multiple developers aren't jockying to check out the same file. The number of checkouts is reduced, so you can now see which ones are the "hot" objects getting frequent revisits. When you want to compile just one piece of your application (which is the crux of your problem here), there is no longer any issue: simply compile the file that changed. There are probably ten more benefits to storing your source code this way, but since I've never had to work in an environment like yours, I'm having a hard time spelling them out as they're taken for granted.
"Smaller" objects that contain no -- or little -- PL/SQL, like synonyms, sequences and types you can keep in aggregated source files, with all the objects collected in one file. We happen to store even those separately.
This WILL make your life easier all around, not just within PSD. Good luck convincing the PTB!!
bc