Merge pull request #188 from wclose/update_lesson_initialize

Updated lesson_initialize

diff --combined bin/lesson_initialize.py
index 757779609994f62f9a0995cf64c41f8c447513de,3f713c9668b894d9e1260a7d7da572eac0f26bbd..acb253b542fc9009602a3c7351352f6b37aeba04
--- 1/bin/lesson_initialize.py
--- 2/bin/lesson_initialize.py
+++ b/bin/lesson_initialize.py
@@@ -89,9 -89,9 +89,9 @@@ from writing new exercises and improvin
  to updating or filling in the documentation
  and and submitting [bug reports][issues]
  about things that don't work, aren't clear, or are missing.
- If you are looking for ideas,
- please see [the list of issues for this repository][issues],
- or the issues for [Data Carpentry][dc-issues]
+ If you are looking for ideas, please see the 'Issues' tab for
+ a list of issues associated with this repository,
+ or you may also look at the issues for [Data Carpentry][dc-issues]
  and [Software Carpentry][swc-issues] projects.
  
  Comments on issues and reviews of pull requests are just as welcome:
@@@ -119,32 -119,30 +119,30 @@@ our lessons must run equally well on al
  
  ## Using GitHub
  
- If you choose to contribute via GitHub,
- you may want to look at
+ If you choose to contribute via GitHub, you may want to look at
  [How to Contribute to an Open Source Project on GitHub][how-contribute].
- In brief:
- 
- 1.  The published copy of the lesson is in the `gh-pages` branch of the repository
-     (so that GitHub will regenerate it automatically).
-     Please create all branches from that,
-     and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
-     before starting work.
-     Please do *not* work directly in your `gh-pages` branch,
-     since that will make it difficult for you to work on other contributions.
- 
- 2.  We use [GitHub flow][github-flow] to manage changes:
-     1.  Create a new branch in your desktop copy of this repository for each significant change.
-     2.  Commit the change in that branch.
-     3.  Push that branch to your fork of this repository on GitHub.
-     4.  Submit a pull request from that branch to the [master repository][repo].
-     5.  If you receive feedback,
-         make changes on your desktop and push to your branch on GitHub:
-         the pull request will update automatically.
- 
- Each lesson has two maintainers who review issues and pull requests
- or encourage others to do so.
- The maintainers are community volunteers,
- and have final say over what gets merged into the lesson.
+ To manage changes, we follow [GitHub flow][github-flow]. 
+ Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
+ The maintainers are community volunteers and have final say over what gets merged into the lesson.
+ To use the web interface for contributing to a lesson:
+ 
+ 1.  Fork the master repository to your GitHub profile.
+ 2.  Within your version of the forked repository, move to the `gh-pages` branch and
+ create a new branch for each significant change being made.
+ 3.  Navigate to the file(s) you wish to change within the new branches and make revisions as required.
+ 4.  Commit all changed files within the appropriate branches.
+ 5.  Create individual pull requests from each of your changed branches
+ to the `gh-pages` branch within the master repository.
+ 6.  If you receive feedback, make changes using your issue-specific branches of the forked
+ repository and the pull requests will update automatically.
+ 7.  Repeat as needed until all feedback has been addressed.
+ 
+ When starting work, please make sure your clone of the master `gh-pages` branch is up-to-date
+ before creating your own revision-specific branch(es) from there.
+ Additionally, please only work from your newly-created branch(es) and *not*
+ your clone of the master `gh-pages` branch.
+ Lastly, published copies of all the lessons are available in the `gh-pages` branch of the master
+ repository for reference while revising.
  
  ## Other Resources
  
@@@ -158,15 -156,14 +156,14 @@@ You can also [reach us by email][email]
  [dc-lessons]: http://datacarpentry.org/lessons/
  [dc-site]: http://datacarpentry.org/
  [discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
 -[github]: http://github.com
 +[github]: https://github.com
  [github-flow]: https://guides.github.com/introduction/flow/
  [github-join]: https://github.com/join
  [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
- [issues]: https://github.com/swcarpentry/FIXME/issues/
- [repo]: https://github.com/swcarpentry/FIXME/
+ [issues]: https://guides.github.com/features/issues/
  [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 -[swc-lessons]: http://software-carpentry.org/lessons/
 -[swc-site]: http://software-carpentry.org/
 +[swc-lessons]: https://software-carpentry.org/lessons/
 +[swc-site]: https://software-carpentry.org/
  '''
  
  ROOT_CONFIG_YML = '''\
@@@ -202,7 -199,7 +199,7 @@@ dc_site: "http://datacarpentry.org
  swc_github: "https://github.com/swcarpentry"
  swc_site: "https://software-carpentry.org"
  swc_pages: "https://swcarpentry.github.io"
 -lc_site: "http://librarycarpentry.github.io/"
 +lc_site: "https://librarycarpentry.github.io/"
  template_repo: "https://github.com/swcarpentry/styles"
  example_repo: "https://github.com/swcarpentry/lesson-example"
  example_site: "https://swcarpentry.github.com/lesson-example"
@@@ -242,8 -239,8 +239,8 @@@ exclude
    - Makefile
    - bin
  
 -# Turn off built-in syntax highlighting.
 -highlighter: false
 +# Turn on built-in syntax highlighting.
 +highlighter: rouge
  '''
  
  ROOT_INDEX_MD = '''\