capitalize all directory names and adapt pathes in files

.gitignore

Documentation/SIP.doc

Documentation/SIP.pdf

Documentation/SUT_ondemand.doc

Documentation/SUT_ondemand.pdf

Documentation/doctrees/Developers/gen_docu.doctree

Documentation/doctrees/Documentation/Api/api_fortran.doctree

Documentation/doctrees/Documentation/Api/api_python.doctree

Documentation/doctrees/Documentation/Input/changes.doctree

...mentation/doctrees/Documentation/Input/compilejob.doctree

Documentation/doctrees/Documentation/Input/control.doctree

...ation/doctrees/Documentation/Input/control_params.doctree

Documentation/doctrees/Documentation/Input/ecmwf_env.doctree

Documentation/doctrees/Documentation/Input/examples.doctree

...ion/doctrees/Documentation/Input/fortran_makefile.doctree

Documentation/doctrees/Documentation/Input/jobscript.doctree

Documentation/doctrees/Documentation/Input/run.doctree

Documentation/doctrees/Documentation/Input/setup.doctree

Documentation/doctrees/Documentation/Input/templates.doctree

...ntation/doctrees/Documentation/Overview/app_modes.doctree