Now we have explicit only used with C++11 and where it should be used.

Now every exception thrown within PLUMED is remapped in the wrapper.

In particular:
- All standard C++ exceptions are remapped to equivalent ones.
- PLUMED exceptions and lepton exceptions are remapped to ad hoc classes.
- Any other exception derived from std::exception is mapped to std::exception.
- Any other exception is rethrown after printing a warning.

I changed Plumed::invalid() to Plumed::makeInvalid() and added a new function
Plumed::makeValid(). These names are more inline with stdlib names
(e.g. make_shared), though with our conventions for capitalization.

Hopefully there's no code yet using this (beta) interface.

In addition, I made it possible to use a macro to change the behavior
of the default constructor to makeInvalid(). This might be
useful in python wrappers to avoid opening the library twice
(python objects always use the "nullary" - default - constructor first).

now covered by the regtest better

It should prepend the libplumed.so library with prefix -Wl,
so as not to disturb NAMD makefile. (suggested by @jcphill)

Should have been removed with 1221e3e1

cc: @dvdesolve

See #407

As of PLUMED 2.4.1, an error is triggered when aligning using a pdb file
with zeros in the last column. I here fix the provided pdb file.

See this:
https://groups.google.com/d/msgid/plumed-users/4e2f69b8-1b2d-4bd3-a2e3-ecdfeef65d77%40googlegroups.com?utm_medium=email&utm_source=footer

I added a plumed_cmd_nothrow function to the interface, that is used from
C++. This allows better support for mixed compilers (e.g. MD code and PLUMED
compiled with different compilers or linked against different std libraries).

Notice that I tried in the past to achieve the same using cmd("setErrorHandler"),
but this does not work correctly with some combination of compilers.
In addition, it implies throwing from a extern "C" function, which is not standard
and might lead to portability issues.

The plumed_cmd_nothrow implementation catches any exception raised within plumed,
converts it to an error code, and rethrows it within the MD code. This approach
should be more robust.

Set LD_LIBRARY_PATH before running plumed when compiling python
interface