./configure --disable-shared was giving an error upon install
due to a missing file

make clean was not correctly cleaning plumed executable

The value of PLUMED_ROOT stored in statically patched MD code was
incorrectly set to the compilation directory rather than the installed one.

The only way to trigger the bug from regtest was by observing the behavior
of rt-make-exceptions when plumed was installed by macports (since in this
case the compilation directory is removed).

Three versions are installed:
plumed - flags to link plumed (as in patch --shared)
plumedWrapper - flag to link plumed wrapper only (as in patch --runtime)
plumedInternals - flags to link full plumed library, including required CPPFLAGS

Notice that some macros are stripped from CPPFLAGS. This might
be improved in order to keep only the relevant ones.

This library contains only the wrapper/Plumed.o object and
can be used to link plumed with --runtime option without
incurring in linking errors when the MD code links PLUMED_LOAD
variables more than ones

This change allows to load libraries locate in src/lib more easily
on a mac. Notice that traditionally this was solved by setting
DYLD_LIBRARY_PATH. However, as of osx Capitan, DYLD_LIBRARY_PATH
does not work correctly. Fixing the installed path with
install_name_tool should solve the issue.

(backported from master)

The new name looks more standard (it is used in the python community)

This fixes the hardcoded path on dylibs

plumed-config was not working (the installer was putting plumed-patch there)

To make the layout more consistent, I made new files:
Config.inc
ConfigInstall.inc
that are generated with a script, whereas:
Config.cpp
ConfigInstall.cpp
are included in the repository.
In this manner all cpp files are included in the repository.

I implemented a shell-only tool "plumed config"

This tool can be used to probe the src/config/config.txt
configuration file.

So far it can be used e.g. as
plumed config has mpi
to enquire for an enabled feature.

It has some advantage wrt the --has-xxx options:

1. It is based on file src/config/config.txt,
which parses configure.ac and header files to find possible -D
and Makefile.conf to find activated -D.
This means that it is not necessary to manually
edit the src/config/Config.h and src/core/CLToolsMain.cpp
file to add new defines

2. it is shell only, thus works in cross compiled environment

This is a textual file that contains all the configuration info.

It should be easier to parse from scripts.

- Implementation of short help (with :PHelp)
- Updated doc
- Autocompletion now knows if label was already provided at the beginning
  of the line and does not suggest it anymore in case
- Compilation of the vim plugin is more similar to compilation
  of the user doc
- Compilation of the vim plugin is made when doing "make install"
  from root dir.

PLUMED_STATIC_DEPENDENCIES was changed in 2.2. I restore here the value that
it had in 2.0 and 2.1 to keep it compatible with cp2k installation procedure

see https://groups.google.com/d/msgid/plumed-users/CAGZMOouB989WaXVd1E8%3DAVmi_BM7EnSpzN7P-NBjR%2BLXjWYV8A%40mail.gmail.com

Since plumed 2.2 creates a directory named src/lib/install
upon install, there could be ambiguity in the install target
in plumed 2.1 when switching branches without cleaning.
Now the target is PHONY, and should give no issue.

This is to avoid using an outdated file

This hack was necessary to support DESTDIR.

Now that all installed files are placed in src/lib/install,
this is not necessary anymore

ask for confirm before deleting files

Do not "make uninstall" on "make install"

This could lead to data loss if prefixes are not properly set

wrong path for uninstall

Fixes #157

* added comments on install paths at the end of ./configure
* fixed include path in modulefile
* make obj/kernel.o only when necessary

Now configure properly takes into account paths such as
--bindir=/path
etc

This implementation hardcodes all the path into the
src/config/ConfigInstall.cpp file. I followed the instructions on autoconf
documentation so that the paths can be changed at install time using e.g.

make install prefix=/path bindir=/path/binxx

This should be the standard behavior.

I removed the possibility to use PLUMED_SUFFIX and PLUMED_LIBPREFIX
since it was a bit too difficult to maintain.

I significantly simplified the src/lib/Makefile by using
the standard directory names for autoconf.

Instead of replicating the whole tree upon install,
now objects are copied to prefix/lib/plumed/obj
and assigned a number.

When possible, objects are grouped in a single kernel.o
with ld -r (tested in configure). This saves a lot
of disk space.

I also removed from the install directory some other
useless files.

The Plumed.inc/cmake files when installing
are generated in a different way from the ones
used prior to installation. Thus, to avoid too many
repetitions, I wrote a small awk script the transforms
Plumed.inc to Plumed.make

Now when plumed is installed the scripts are placed in
lib/plumed/
instead of
bin/

This makes it more robust the installation of several versions with suffixes

I only left in place the script "plumed-patch" which is likely
the most used.

I added plenty of messages at the end of ./configure and make install
+ I explained it in the user doc

Now command line shortcuts such as plumed-patch
follow the same rule as plumed executable to set PLUMED_ROOT
as it was implemented in 1b20cb90

Namely, they have an hard coded value that can be replaced
setting the PLUMED_ROOT variable before launching the tool

Now plumed should work if built on a directory which has a space in the path.
Notice that install directory should still not contain spaces.
This is because of some difficulties in making the
src/lib/Makefile rules compatible with names with spaces.

Addresses #157

Added support for DESTDIR

We usually allowed users to customize the name of the plumed
library using env var PLUMED_LIBSUFFIX. I changed it to the
standard autoconf behavior, that is using
--program-suffix
--program-prefix
at configure time.

PLUMED_LIBSUFFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

Before this fix, the PLUMED_KERNEL env var was erroneously not
containing the LIBSUFFIX value.

This fix is relevant only if one use at the same time PLUMED_LIBSUFFIX
*and* loads the module file, which is unlikely.