I renamed all files from .txt to .md so that they can be
visualized on github.

In addition, I renamed all files to have a name consistent with the content.
This makes manual portions easier to find.

Notice that I left the original labels (e.g. "Syntax" instead of "Getting Started")
not to break direct links to manual, though I think we should rationalize these names
as well.

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- added FMT keyword
- added regtest

added a two regtests
close #243

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Thanks to Sean Marks

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# Conflicts:
#	regtest/crystallization/rt-q6/colv.reference

# Conflicts:
#	configure
#	configure.ac

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Output is very similar but it looks like it gives many less warnings
in the log.

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- munster
- moving

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See #239

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