Fix sloppy commit from https://rbcommons.com/s/twitter/r/901/

Testing Done:
Did a test publish from a Twitter monorepo.

Reviewed at https://rbcommons.com/s/twitter/r/940/
bad troubleshooting instructions: kicking 'em when they're down :-(
But that's what we're doing:

./pants -ldebug goal goals
Invalid command: -ldebug

Reviewed at https://rbcommons.com/s/twitter/r/953/
Refactor exceptions in build_file.py and build_file_parser.py to derive   from a common baseclass and eliminate throwing IOError. Catch errors from parse errors in the BUILD file and format   context around the exception.

Followon to https://rbcommons.com/s/twitter/r/929/

Refactor exceptions in build_file.py and build_file_parser.py to derive from a common baseclass and eliminate throwing IOError.

Revive error message that prints out alternatives to an incorrect build target.

Also, Catch exceptions from parse errors in the BUILD file and print some formatted context around the line of the file that failed.

Exception message: Error parsing /Users/zundel/Src/Pants/examples/src/java/com/pants/examples/hello/greet/BUILD:
    4: java_library(name = 'greet',
    5:   dependencies = [], # A more realistic example would depend on other libs,
    6:                      # but this "hello world" is pretty simple.
*   7:   sources = globs('*.java' && foo),
                                   ^ SyntaxError: invalid syntax (<string>, line 7)

    8:   provides = artifact(org='com.pants.examples',
    9:                     name='hello-greet',
   10:                     repo='build-support/ivy:public',),
   11: )

Testing Done:
ci passed at https://travis-ci.org/pantsbuild/pants/builds/33756154

Bugs closed: 537

Reviewed at https://rbcommons.com/s/twitter/r/954/
Add tests for junit_run._JUnitRunner; fix a regrsssion in Emma/Cobertura; refactor exclusive_groups prep to base_test.

- Add test for junit_run._JUnitRunner class (specially testing against future regression in https://github.com/pantsbuild/pants/issues/508).
- Fix a regression introduced in last fix that impacted Emma and Cobertura (reported by jayeye)
- Refactor populate_exclusive_groups into base_test so tests (test_jvm_run and test_junit_run and others) can reuse it.

Testing Done:
- Travis CI: https://travis-ci.org/jinfeng/jinfeng-pants-fork - CI passed.

- Local run:

$ PANTS_DEV=1 ./pants goal test tests::

============== test session starts ===============
                     platform darwin -- Python 2.6.8 -- py-1.4.23 -- pytest-2.5.2
                     plugins: cov, timeout
                     collected 500 items
                     ...
                     ...
                     tests/python/pants_test/backend/jvm/tasks/test_junit_run.py .
                     ...
                     ...
                     tests/python/pants_test/tasks/test_jvm_run.py .
                     ...
                     ...

                      490 passed, 5 skipped, 5 xfailed in 413.71 seconds

16:45:57 07:37     [junit]
16:45:57 07:37     [specs]
               SUCCESS

Bugs closed: 508

Reviewed at https://rbcommons.com/s/twitter/r/935/
Add IntelliJ content type to project Info. Add missing resources to targets.

This is required for intelliJ pants plugin to correctly mark the source, resource, test target and test resources.

The constants are defined here in IntelliJ
http://grepcode.com/file_/repository.grepcode.com/java/ext/com.jetbrains/intellij-idea/13.0.0/com/intellij/openapi/externalSystem/model/project/ExternalSystemSourceType.java/?v=source

Testing Done:
Locally ./pants tests/python/pants_test/tasks:depmap passes

https://travis-ci.org/pantsbuild/pants/builds/33880605

Reviewed at https://rbcommons.com/s/twitter/r/964/
jar_library docstring += dependencies

eagle-eyed J.I. Ioannidis noticed that our 3rdparty JVM docs show jar_library(dependencies=) but the BUILD dictionary doesn't (at least, I think that's what's going on)

until we fix https://github.com/pantsbuild/pants/issues/142, add doc for this param by hand, like an animal

Reviewed at https://rbcommons.com/s/twitter/r/960/
add include-excerpt feature to 'goal markdown'

Extend markdown syntax so that page authors can "include" a snippet from a real source file. Inspired by the way the Pants docs use Spinx's literalinclude http://sphinx-doc.org/markup/code.html#directive-literalinclude .

Added docs for it in src/python/pants/docs/page.rst

Exercise it in examples/src/java/com/pants/examples/hello/main/README.md

Testing Done:
Added test_markdown_to_html.py with a bunch of tests for the "excerpt a few lines" functionality, which has corner cases.

https://travis-ci.org/pantsbuild/pants/builds/33925158

Reviewed at https://rbcommons.com/s/twitter/r/949/
Move the jvm_compile/java IT from unit to IT.

Noticed this one very slow test when running the unit tests via :all which is not dead yet.

Testing Done:
CI went green here: https://travis-ci.org/pantsbuild/pants/builds/34067665

Bugs closed: 542

Reviewed at https://rbcommons.com/s/twitter/r/970/
Fixup engine test deps.

I was starting to look at coveralls and ran into some missing deps on my chosen victim test target, this fixes the deps up.

Testing Done:
```console
$ PANTS_PY_COVERAGE=1 ./pants goal test tests/python/pants_test/engine
$ PANTS_PY_COVERAGE=1 ./pants goal test tests/python/pants_test/engine:test_engine
$ PANTS_PY_COVERAGE=1 ./pants goal test tests/python/pants_test/engine:test_round_engine
$ COVERALLS_REPO_TOKEN=XYZ coveralls
```

https://coveralls.io/jobs/2668487

CI went green here: https://travis-ci.org/pantsbuild/pants/builds/34040483

Bugs closed: 369, 540

Reviewed at https://rbcommons.com/s/twitter/r/968/
Add a whitelist to jvm dependency analyzer

The whitelist allows big repos to reduce dependency issues while stopping any new from being introduced. You can whitelist the projects that currently have issues and make the dependency checks fatal. All projects with current issues will still be able to build but new issues will result in breaking builds.

Also it seems like the direct dependency check would always fatal if set to fatal, fixed that.

Testing Done:
Added two integration tests.

Reviewed at https://rbcommons.com/s/twitter/r/888/
Fixed source roots in project info for IntelliJ plugin in case of ScalaLibrary with java_sources

Testing Done:
CI is passing.

Reviewed at https://rbcommons.com/s/twitter/r/955/
Fix the --ivy-report option and add integration test

I inadvertently broke this back at https://rbcommons.com/s/twitter/r/941/ by  removing the override from pants.ini
I went back and audited other bootstrap-tools references and made them absolute address specs and made sure they were surrounded in '[]'

Testing Done:
CI passed, invoking with --ivy-report manually from the command line no long throws an exception and creates a report.

Bugs closed: 545

Reviewed at https://rbcommons.com/s/twitter/r/976/
Add Coveralls code coverage badge

https://coveralls.io/r/pantsbuild/pants
predictable output path for 'goal markdown'.

Instead of outputting to .pants.d/something/... , generate to dist/markdown

(A Twitter team was smooshing Task code into a BUILD file to tweak page generation.
This here change aims to generate .html in a predictable place.
So that Twitter team (or maybe I) can scriptily modify that .html _not_ in a BUILD file, sheesh.)

Testing Done:
https://travis-ci.org/pantsbuild/pants/builds/34236236

and added a test

Bugs closed: 535

Reviewed at https://rbcommons.com/s/twitter/r/961/