Fixed checkout message when working tree is not clean, suggesting using --force option
Merge pull request #69 from volaya/conflicts_command

Replaced MergeTools command by Conflicts command and added test
Merge pull request #68 from volaya/apply_fix

fixed problem with apply command using object database instead of stagin...
Fix functional test failure introduced at b9156bef7
Implemented missing case in merge operation (auto-merged features)

This commit also includes some refactoring/renaming to make merge steps and operations clearer and to allow being used in different contexts
Code cleaning has been perfomed and headers have been added to classes that were missing them
Added conflicts support in cherry-pick operation
Added support for rebase operation with conflicts

Also Added documentation for rebase operation and --squash option