git prompt: Fix hang on detached head.

$git_dir was never set in __fish_git_prompt_current_branch, but used
in the case of a detached HEAD.  This caused `cut -c1-7 $git_dir/HEAD`
to expand to `cut -c1-7` which then waited for input.
Mark jobs as completed when all processes have finished, not just the last one.
Fixes https://github.com/fish-shell/fish-shell/issues/876 , and coincidentally also https://github.com/fish-shell/fish-shell/issues/848
Fix for incorrect use of shared ptr references
Cleanup of code that decides whether or not to fork. Fix for issue where stderr may be output twice.
Added completions for Vagrant
Portmaster completions

* Added FreeBSD's pkg to __fish_print_packages
* Portmaster completes on installed packages and ports
* Options list as per fish_generate_completions, needs to be tidied
  up further but will suffice for now
Fix variable name
Informative version of __fish_git_prompt_show_upstream
Added informative status method
Fixes, new method added to prompt
Use tabs, sample prompt
Less code is better, __fish_git_prompt_validate_colors refactor
Support for defining color with bold/brighter color set
Renaming, cleanup
Less code is better, __fish_git_prompt_validate_chars refactoring
docs: configure/Makefile changes to require at least Doxygen 1.5
Add completion for Bundler

Signed-off-by: David Celis <me@davidcel.is>
Put user paths at beginning
Update documentation for $fish_user_paths
Cleaned up commented lines and updated method names in create_manpage_completions script