get examples to run as tests too, one is currently broken
clean up docs a bit
forgot main doc file
add link to rmf_examples
Update README.md
Update README.md
add rmf_pdb that doesn't require IMP
Merge branch 'develop' of github.com:salilab/rmf into develop
use locks for in all executables
forgot the lock command
remove FileLock
Update README.md
Update README.md
use locks for in all executables
forgot the lock command
remove FileLock
Move the frame number from an argument to functions to a state for the File

The frame is now changed by calling set_current_frame(), get_current_frame() on the file, rather than simply passing the frame when setting a value. This will allow files to have a sense of the current frame and so support caching and other optimations based on it.
use better place for include path
Squash sets into the node hiearchy

There are no more separate set properties (eg for bonds). Instead, a bond is a node with two children and type bond. Nodes can now be the child of more than one parent. An alias is used internally to provide the second parent. This allowed me to delete lots of code and will make other backends much easier.
resolve merge