PlumedFile's were not flushed correctly

Attempt to solve the problem of incomplete HILLS file. Seems to be working, but need some revisions and discussions with you guys…

I added a method to reset the EOF indicator of a stream. Needed by multiple walkers. Still is not working properly when one walker is reading an incomplete line (because it is being written) from another walker's file.  In these cases, I got:
+++ Internal PLUMED error
+++ file PlumedFile.cpp, line 311, function PLMD::PlumedIFile &PLMD::PlumedIFile::advanceField()
+++ message: assertion failed nf==words.size()

While trying to use the new printField stuff for metadynamics I
realized that it is simpler if one does not need to explicitly
declare which fields will be printed.

I added a class for reading (PlumedIFile),
fixed a few problems in the PlumedOFile, improved
documentation. Still it is not completely tested.

Documentation is still a bit poor. I used it to replace
the Log implementation and also for in the GenericPrint class.
In the log, this implies a small change (FIELDS line is
written in also in the log).

I tried to make everything so that regtests are not affected. Only,
change, now the rt17 (using _ROTATE) works correctly, writing
field names as they are updated.