Fixed NPE on jar/war files without manifest
Allowing preparedPaths to be true even if there are errors.

This change means that if there are TONS of errors, the project won't be
reprocessed over and over and over again. A simple way to see where
this would be a problem is if you had many projects that included
each other in their buildpaths. Now remove one of the foundational
projects from your workspace -- actually delete the files, not
just delete the eclipse project. the Project class will get hung up
because it continues to process all Projects because none of them
are ever "Ok".
More trace on certs and a method to get a url
Added MacOS list VM support. This needs to be extended
improved stack trace
Improved table formatting
Added method that gathers files from a directory
Can use recursive and path or name based matching
Added a compile command
Added a compile command
Added the convent of build phases
Build phases model the actions you can execute on
a project or a build. Since these normally are very
specific for a build, the model is quite flexible.
There is a DefaultPhases that uses the standard
build model thingies. PhasesPlugin plugins can be
registered to provide additional phases which
are called in ranking order and then should call
their later siblings.
Provide utility methods for flattening a list of containers
Flattening is required because Container objects can have
members if they are libraries
Improved printing of the exceptions
test removed
Added pack command
Fixes
Some extra tests
Fix. Used java.source and not javac.source, also for other
properties.
#473 close. Flattened properties are not completely expanded.
Properties that start with a minus sign are not processed, so they still contain the macro
Properties that start with an '_' are not included at all.

Adapted the comment and added a new method that can be used to do the full expansion
Added more threads to the default thread pool
Some fixes in the compile code
- debug is currently a boolean, can now ALSO set the debug option
- Projects without sources caused errors