Partial credit goes to Vedran Miletić <vedran@miletic.net> for cleaning
up and fixing the parts of the text.

This solves the download issues which started when Eigen finalized the
move from Bitbucket to GitLab and removed the old repo on Bitbucket.

Eigen 3.3.8 is already out, but it suffers from the compilation issues
and can't be used: libeigen/eigen#2011

Added Tabularize command for easy conversion to CSV using CLI.

Added Transform command that replaces a number of Perl scripts used
for sorting, naming, and filtering with the goal to eventually replace
all presently bundled Perl and Python scripts.

The public API should be considered work in progress at this point. At
the time of the stable release, the public API will support a number
of operations and will remain stable over time as the internal program
structure continues to change.

Also removed unused headers from Rbt.h and related Config.h.

Headers are now in include/rxdock/, implementations in lib/, executables
in tools/, and tests are in tests/ with data in tests/data/.

Removed BaseObject::{Get,Set}Trace functions and TRACE configuration
directives from parameter files.

Also added wraps for Loguru and {fmt}.

Partial credit goes to Luka Vretenar <luka.vretenar@gmail.com> for
helping with the grunt work of the conversion.

Also removed obsolete building and installation instructions.

Used nlohmann_json for JSON input and output.

Specifically, chrom, program, ri, and tethered_atoms are now lowercase
fields prefixed with rxdock. (e.g. rxdock.ri, rxdock.chrom.0).

Updated data files accordingly and renamed functions and methods as
necessary where conflicts occured.

Renamed functions where conflicts occured and added out of class
declarations for some operators that were previously declared only as
friends in classes to silence GCC warnings and fix MSVC errors. In
particular, renamed rxdock::GetVersion() to rxdock::GetProgramVersion()
to avoid conflicts with Win32 API function from <sysinfoapi.h> header.

Index variable 'i' in OpenMP 'for' statement in RbtDockingSite must
have signed integral type.

In particular, replaced std::unary_function, std::binary_function, and
std::ptr_fun with std::function, std::bind2nd with std::bind, and
std::mem_fun_ref with std::mem_fn.

That occurence of rDock was wrongly generalized to |Dock| (so it can be
rDock or RxDock depending on the value of the replacement text).

Thanks to Sergio Ruiz Carmona <Sergio.RuizCarmona@baker.edu.au> for
spotting this mistake and reporting it.

Also changed one wrong occurence of rDock in the User guide to |Dock|,
where we link to download links for RxDock.

This yields more performance; in multiple tests I measured about
10-12% speedup using rbcavity.

The matrices used are self adjoint so the SelfAdjointEigenSolver
performs better than the generalized one.

In the test performed by the command:

rbdock -r 1YET_test.prm -i 1YET_c.sd -p dock.prm -n 2 -s 48151623 -o
1YET_test_out

the SelfAdjointEigenSolver saved about 8% of total execution time
(measured with the function profiler).

- default constructors
- std::string references
- std::move in constructors
- auto& and range-based for loops