Delete 'include' folder and reorganize headers.

* Place headers in the same folder as the sources.
* Include folder src/ while compiling, to access common headers.
Make certain parameters in input files optional.

* All the moving body options in bodies.yaml.
* scaleCV, restart and startStep in simParams.yaml.
* initialPerturbation in flow.yaml.
* Edit input files for impulsively-started cylinder cases.
* Input interpolation type for Eulerian direct forcing methods.
* Print time-stepping schemes and interpolation type at the beginning.
Remove default CL options from cavityRe100.py.

* Run with options prescribed in input files instead of defaults.
* Include interpolationType in all DirectForcing and FadlunEtAl cases.