I think this closes #146

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I added an example similar to the one that I provided
on the mailing list about how to mimick
POINT_FROM_AXIS and PROJ_ON_AXIS

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If not, tracking is disabled. Notice that we might want
to allow one to set different flags in the future.

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In this manner quotes are not required in -D
making its syntax simpler

This cpp macro allows one to set a default path for the PLUMED_KERNEL.

Useful while patching in macports

I fixed a complain of cppcheck which discourage using
find()==0

This will allow upgrading to latest cppcheck.

useful for macports

[makedoc]

Now works also when plumed has been installed with a different name

- METAD: exit with error if used
- PBMETAD: gives a warning and deactivate the interval for the specific variable
close #181

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I think this fixes #143

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fix a problem when md.log was appended
plumed was trying to write on it after
md.log was already closed

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