Added issue and pull request templates

.github/ISSUE_TEMPLATE.md

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+### Instructions
+
+- Use a **concise** yet **descriptive** title;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;
+- If the issue will be added to the public tracker (using the `public` label), it must conform to [these guidelines](http://gatkforums.broadinstitute.org/dsde/discussion/6801/guidelines-for-tagging-issues-with-the-public-tag#latest);
+- Delete the other template blocks and this header.
+
+----
+
+## Bug Report
+
+### Affected tool(s)
+_Tool name(s), special parameters?_
+
+### Affected version(s)
+- [ ] Latest public release version [version?]
+- [ ] Latest development/master branch as of [date of test?]
+
+### Description 
+_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._
+
+#### Steps to reproduce
+_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem on a test case on one of the gsa* servers._
+
+#### Expected behavior
+_Tell us what should happen_
+
+#### Actual behavior
+_Tell us what happens instead_
+
+----
+
+## Feature request
+
+### Tool(s) involved
+_Tool name(s), special parameters?_
+
+### Description
+_Specify whether you want a modification of an existing behavior or addition of a new capability._
+_Provide **examples**, **screenshots**, where appropriate._
+
+----
+
+## Documentation request
+
+### Tool(s) involved
+_Tool name(s), parameters?_
+
+### Description 
+_Describe what needs to be added or modified._
+
+----

.github/PULL_REQUEST_TEMPLATE.md

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+### Description
+
+_Please explain the changes you made here._
+_Explain the **motivation** for making this change. What existing problem does the pull request solve?_
+_Mention any issues fixed, addressed or otherwise related to this pull request, including issue numbers or hard links for issues in other repos._
+
+----
+
+### Checklist (never delete this)
+
+Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below. 
+
+#### Content
+- [ ] Added or modified tests to cover changes and any new functionality
+- [ ] All tests passing on Bamboo (including license tests!)
+
+#### Form
+- [ ] Rebased, squashed and reworded to produce a single commit (exemptions may be made -- sparingly) that is _uncluttered by excess lines_ (lines that just say "addressed review", "fixed" etc left over from squashing)
+- [ ] Both the PR and the final rebased commit have a **concise** yet **descriptive** title (they are used when we compile version notes)
+- [ ] Edited the README / documentation accordingly and got sign-off from support team (private code is exempt)
+
+#### Review
+- [ ] Suggest a reviewer or ask your team lead to suggest one
+- [ ] Final (thumbsup) from the reviewer(s)
+
+Once everything is checked off, you can go ahead and merge the PR. Don't forget to also delete the branch.

.gitignore

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+.idea/
+.queue/
 /*.bam
 /*.bai
 /*.bed
 *~
 /*.vcf
 /*.txt
 /*.csh
-/.*
 /*.pdf
 /*.eval
 *.ipr
 *.iws
 *.iml
 *.pyc
 .DS_Store
-queueScatterGather
 /foo*
 /bar*
 integrationtests/
-public/testdata/onTheFlyOutputTest.vcf
 build/
 dist/
 dump/