Adding a dependency from a java_library to a scala_library, this should not trigger the build dependency missing warning.

Jmake's analysis file only contains the dependency class names, not the full path to the class file. This means it assumes
they are in the compiled java directory, meaning we get missing dependency warnings for scala files.

Changed to pick those up in the correct classes directory.

Reviewed at https://rbcommons.com/s/twitter/r/474/
Fix erroneous binary dependency for the bundle goal.

Testing Done:
Using `PANTS_DEV=1 ./pants goal bundle {src,tests}/{java,scala}::`

Before:
=======
3.862	main:binary
3.540	main:binary:binary
3.517	main:binary:binary:create-monolithic-jar
3.266	main:binary:binary:create-monolithic-jar:jar-tool
1.631	main:jar
1.624	main:jar:jar
1.618	main:jar:jar:jar-create
1.505	main:jar:jar:jar-create:jar-tool
1.368	main:resolve
1.363	main:resolve:ivy
1.280	main:resolve:ivy:map-jars
0.661	main:bundle
0.654	main:bundle:bundle
0.624	main:bundle:bundle:create-monolithic-jar
0.464	main:bundle:bundle:create-monolithic-jar:jar-tool

After:
======
1.419	main:jar
1.413	main:jar:jar
1.402	main:jar:jar:jar-create
1.327	main:resolve
1.322	main:resolve:ivy
1.295	main:jar:jar:jar-create:jar-tool
1.236	main:resolve:ivy:map-jars
0.638	main:bundle
0.632	main:bundle:bundle
0.605	main:bundle:bundle:create-monolithic-jar
0.442	main:bundle:bundle:create-monolithic-jar:jar-tool

Bugs closed: 219

Reviewed at https://rbcommons.com/s/twitter/r/513/
Divorce 'binary' and 'bundle' goals from the 'jar' goal.

Save effort and time by extracting classfile jar creation
logic to JarTask and using this in JarCreate and JvmBinaryTask
to create classfile jars directly.  Previously BinaryCreate and
BundleCreate re-packed jars containing internal classes created
by the JarCreate Task.  Now time is saved by not creating these
middle-man jars at all.

Testing Done:
$ PANTS_DEV=1 ./pants goal test tests/python/::

Then:
Using `PANTS_DEV=1 ./pants goal bundle {src,tests}/{java,scala}::`

Before:
=======
1.419	main:jar
1.413	main:jar:jar
1.402	main:jar:jar:jar-create
1.327	main:resolve
1.322	main:resolve:ivy
1.295	main:jar:jar:jar-create:jar-tool
1.236	main:resolve:ivy:map-jars
0.638	main:bundle
0.632	main:bundle:bundle
0.605	main:bundle:bundle:create-monolithic-jar
0.442	main:bundle:bundle:create-monolithic-jar:jar-tool

After:
======
1.479	main:resolve
1.473	main:resolve:ivy
1.383	main:resolve:ivy:map-jars
0.708	main:bundle
0.701	main:bundle:bundle
0.669	main:bundle:bundle:create-monolithic-jar
0.493	main:bundle:bundle:create-monolithic-jar:jar-tool

IE: 1.419 seconds of JarCreate time cut out, and 0.063 seconds of Bundle time added.

I also verified binaries and bundles were still runnable and had embedded resources where they did before this change.

Bugs closed: 220

Reviewed at https://rbcommons.com/s/twitter/r/514/
Bump default versions of setuptools and wheel

Testing Done:
CI passes

Reviewed at https://rbcommons.com/s/twitter/r/517/
Relativize java classpaths relative to the build root

JIs original relativization code didn't work because java was executed with subprocess.call, and this call was given a different cwd argument (the build root) than the user's actual current working directory. I have made the classpaths relativized relative to the build root as opposed to the current working directory, and this seems to work.

Also added classpath length logging (so we can know when we are getting close to the maximum argument length).

Testing Done:
./build-support/bin/ci.sh all tests passed

Reviewed at https://rbcommons.com/s/twitter/r/516/
doc: Pants Internals += source roots

attempting to capture some generally-useful info from https://groups.google.com/forum/#!topic/pants-devel/FhS8k4QDJN8

Bugs closed: 186

Reviewed at https://rbcommons.com/s/twitter/r/496/
Fix test for python 2.6, add a few more checks
rename test and move to appropriate place
rename test, add docs, make one fix to builddict
Merge branch 'master' of https://github.com/pantsbuild/pants into areitz/pants/fix_wiki
remove some test code
remove bad comment from merge
remove some more debug code
remove dangling comma
Use setuptools 5.0 (==3.8.1) because of a regression in 4.0.1

See https://rbcommons.com/s/twitter/r/517/ and
https://mail.python.org/pipermail/distutils-sig/2014-June/024478.html

Testing Done:
CI passed

Reviewed at https://rbcommons.com/s/twitter/r/520/
Merge branch 'master' of github.com:pantsbuild/pants into areitz/pants/fix_wiki