Fixed maximum number of sims running.

Before it started one sim more that specified by maxSimThread.
Added support for "auto" mode for maxSimThreads.
Made the "general.cfg" to "default.cfg".

That means that the new "default.cfg" will ALWAYS be parsed before the
user specified config (via -c or --config). This will make changing
settings easier and does not break so easily on switching revisions of
"default.cfg".
So please don't push any custom versions of the default configuration to
the repo if it should not really affect the default behaviour for all
users. In fact don't edit it at all except for changing the default
behaviour of this program.
The simulation path is now under results.

Until now the default was to create a temp folder, but this was not the
best solution because of data loss or log files missing the last lines
because of the copying. It was also possible to force "in source" builds
that messed up the neuroConstruct project templates.

So finally the simulations have been moved for more cleanliness
and are by default under the results subdirectory (configurable).

The previous default can still be achieved using the -t or --temp option
to create the tmp folder before moving the results to the results
subdirectory.
Removed obsolete .gitignore entries.

It is no longer possible to generate the files and folders in the
removed entries, so they have been removed to better see impure project
folders.

Any files under Pyr_* will be copied to the simulation path when
starting the program, so they should remain clean.