Backport from other branches

[Thrameos]

This is a backport of changes from future branches.

• Fixes warnings on clang.
• Removes thunk code and replaces with external jar file.
• Adds a dynamic class loader to loading classes after the JVM is started.
• Fixes name conflict on overloaded method.
• Internal jar is now available regardless of how it was loaded.
• Adds attach to JVM entry point for starting Python from Java or Android.
• Native entry points now load automatically rather than being registered manually.

[codecov]

Codecov Report

Merging #802 into master will increase coverage by 9.36%.
The diff coverage is 100.00%.

@@             Coverage Diff              @@
##             master     #802      +/-   ##
============================================
+ Coverage     83.06%   92.42%   +9.36%     
============================================
  Files           142       24     -118     
  Lines         11813     1453   -10360     
  Branches       4454        0    -4454     
============================================
- Hits           9812     1343    -8469     
+ Misses         1248      110    -1138     
+ Partials        753        0     -753     

Impacted Files	Coverage Δ	Complexity Δ
jpype/_core.py	96.19% <100.00%> (+0.03%)	0.00 <0.00> (ø)
jpype/pickle.py	88.09% <100.00%> (-0.55%)	0.00 <0.00> (ø)
jpype/_jstring.py	96.87% <0.00%> (-3.13%)	0.00% <0.00%> (ø%)
jpype/_jclass.py	98.46% <0.00%> (-0.77%)	0.00% <0.00%> (ø%)
native/common/jp_gc.cpp
native/python/pyjp_char.cpp
native/common/jp_stringtype.cpp
native/common/include/jp_array.h
native/common/jp_primitivetype.cpp
...ative/java/org/jpype/javadoc/JavadocException.java
... and 62 more

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[Thrameos]

This is targeting release 1.1.x as it does things to the backend that constitute a substantial change (though it shouldn't be reflected in the API.) It will take a while to get all the bugs out as it touches the boot loader path. After this point we won't have to do special magic to register the native entry points and our jar file will be accessable outside the module (which doesn't do much until I complete the rest of Python from Java patch.)

[Thrameos]

@marscher This one is finally ready for review. This won't be applied until 1.1 as it is rearranging stuff having to do with thunks. It is a prerequisite for a few future enhancements as it cleans up a bunch of core issues and makes native linking much easier.

[Thrameos]

Working to resolve the conflict. Will take a bit as it is a structural difference in the load procedure that needs to be resolved.

[Thrameos]

Is this review complete?

[marscher]

Sorry I've added some points in the meantime.

[Thrameos]

@marsher So I have added a bunch of PRs that could go in that could form a patch release as well as few that are built on this as a base. I have tried to label which are which by the milestone. If you see something that isn't appropriate for a patch release you can add the milestone to it. So we may need to come up with some other way to indicate it.

In the mean time, I have been trying to identify some of the user needs by soliciting input from some of the other github projects. Bayer-Group/paquo#33 and scijava/scyjava#18. It has given me a few ideas that we may be able to apply.

[pelson]

Awooga! I just bisected an issue (to be raised shortly) which points back to this commit. I have no idea if the problem is related to this, but I was quickly reviewing the code and saw this. I'm sure you already know about the pitfalls of mutable defaults with Python, and that they are a no-go unless you really intend them.

[pelson]

The other mutable defaults in Platform appear to have been removed in 1f58b10.

Issue mentioned opened in #848. Unfortunately, fixing this one doesn't seem to address