My project directory is something like
src
ProjectName
Package1
__init__.py
Module1.py
Module2.py
Package2
__init__.py
Module3.py
Moduel4.py
__init__.py
main.py
setup.py
When I do Project->Clean..., PyLint runs, but only on the three files in the uppermost package: __init__.py, main.py, and setup.py.
I have gone into Project->Properties->PyDev - PYTHONPATH, and all of the source folders are definitely listed there, so I'm not sure why most of them aren't being analysed.
Also, like this question, PyDev doesn't seem to be parsing the PyLint output, as the errors and warnings that show up in the console aren't in the 'Problems' output tab, or in the editor margins. This makes me think it might be a version/regression problem, as it was for that question. I might try an older version of PyLint and see if that works.
I'm using Eclipse Helios, PyDev 2.2.1, PyLint 0.25.1, and Python 2.7.
The PyLint configuration (window > preferences > pydev > pylint), has a 'maximum number of processes for PyLint', so, it'll only run analysis on 'n' files simultaneously (because spawning too many processes at once could bring your machine to a halt).
So, you can raise that number for the analysis and and it should analyze more files at once (I'd recommend raising it for that analysis and then reducing the number again, as you don't usually want too many processes running at once).
As for the output, it could be that PyLint changed its format (please report that as a bug in the pydev sourceforge tracker if you believe that's the case).