indent to two spaces

This patch contains only whitespace changes, plus a short
addition to CONTRIBUTING.md on the project-wide indent style
refactor bash scripts into functions

add some comments
always use full path to external utilities

per #2029
rename nethack-cocoa.rb

to nethackcocoa.rb
per naming rules in CONTRIBUTING.md
rename google-app-engine-launcher.rb

to googleappenginelauncher.rb
per naming rules in CONTRIBUTING.md
rename cocoa-packet-analyzer.rb

to cocoapacketanalyzer.rb
per naming rules in CONTRIBUTING.md
rename sql-explorer.rb

to sqlexplorer.rb
per naming rules in CONTRIBUTING.md
rename comic-book-lover.rb

to comicbooklover.rb
per naming rules in CONTRIBUTING.md
rename comic-book-lover-sync.rb

to comicbookloversync.rb
per naming rules in CONTRIBUTING.md
dupe of Cask cloudpull.rb (the correct name)
Add Adobe Reader v11.0.06
Merge pull request #2575 from miguelfrde/adobe-reader

Add Adobe Reader v11.0.06
Merge pull request #2574 from rolandwalker/rename_comic-book-lover-sync

rename comic-book-lover-sync.rb
Merge pull request #2573 from rolandwalker/rename_google-app-engine-launcher

rename google-app-engine-launcher.rb
Merge pull request #2571 from rolandwalker/remove_dupe_cloud-pull

dupe of Cask `cloudpull.rb` (the correct name)
Merge pull request #2570 from rolandwalker/rename_cocoa-packet-analyzer

rename cocoa-packet-analyzer.rb
Merge pull request #2572 from rolandwalker/rename_nethack-cocoa

rename nethack-cocoa.rb
Merge pull request #2569 from rolandwalker/rename_sql-explorer

rename sql-explorer.rb
Merge pull request #2568 from rolandwalker/rename_comic-book-lover

rename comic-book-lover.rb
Merge pull request #2566 from rolandwalker/full_paths

always use full path to external utilities