Review request: jpkg -m option takes both classes and resources

[Mandy Chung]

The jpkg command currently takes the -m option to specify the directory 
containing the classes for a module and takes the -r option to specify 
the directory containing the resources.  Classes and resources must be 
in separate directory which is different than what we (Java developers) 
generally do (compiled classes and resources are placed in the same 
build directory).  To create a jmod file from an existing Java project, 
it has to separate the classes and resources from a build directory to 
run the jpkg command which is rather annoying.

This change removes the -r option and have the -m option to take both 
classes and resources.

Webrev:
     
http://cr.openjdk.java.net/~mchung/jigsaw/webrevs/jpkg-dash-r-option.00/

Many files and tests are touched due to the rename of ModuleFileFormat 
to ModuleFile and ModuleFileFormat.Writer to ModuleFileWriter.  Since 
several tests are updated for this change, I took the chance to change 
-source 7 to -source 8 and update other tests as well.

The main change is:
1.  ModuleFileWriter (was ModuleFileFormat.Writer) - I refactored the 
existing implementation so that it can process a given directory of both 
classes and resources in a clean way.
2. Rename ModuleFileFormat to ModuleFile and I leave the Reader 
implementation as it is.  Sean mentioned in the past that the ModuleFile 
class should be made immutable and need some clean up.  Some work to be 
done in the future.
3. Rename the ModuleFormatTest01.java to ModuleFileTest.java.   I 
rewrote half of the code and keep some existing utility functions.  The 
new ModuleFileWriter implementation only  writes a CLASSES section if 
there is at least one class file other than module-info.class.  I had to 
fix this test as the existing implementation always creates a CLASSES 
section which is a bug.  But there is no clean solution.  Also initially 
the test tests both regular jmod files and signed jmod files which 
duplicates the code.  I changed ModuleFileTest.java to take an input 
argument and if set, it will run the same set of test cases but sign the 
jmod file.  So ModuleFileTest.java is now a jtreg test to test regular 
jmod file and SignedModuleFileTest.sh will run ModuleFileTest with an 
input argument to test the sign jmod file case.

Thanks
Mandy