Move readFile() and writeFile() to new class FileIO.
Read input through YAML file also in batch version.

(also remove unused lines of code)
Set duration in YAML file.

Also mark some functions as deprecated.
Merge pull request #88 from aipp/file2

Read input from YAML file also in batch version
Merge branch 'upstream' into file

Conflicts:
	pixi/input/One_particle_Test.yaml
	pixi/input/Pair_of_particles.yaml
	pixi/input/Two_stream_instability.yaml