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* Support kernel files with extensions of any length (like .hip)

* Do not allow to replace symbols in single-line comments

* Add OPENMM_BUILD_COMMON CMake option

It allows to build and install common platform files even if
CUDA or OpenCL platforms are not built.
This is required for HIP platform (openmm-hip) if ROCm OpenCL
packages are not installed.

* Add an option for Python wrapper to install into user packages

OPENMM_PYTHON_USER_INSTALL is OFF be default.

* Support FFT backends in Amoeba plugin

The HIP platform supports FFT backends, this commit moves
findLegalFFTDimension to ComputeContext, so platforms can have their own
implementations.

* Compatibility for common platform w/ new HIP platform

* Do not use volatile with private and local AtomData parameters on HIP

The generated code is not optimal, for example, the compiler generates
flat_load instructions instead of ds_read.

* Tune launch bounds for PME grid-related kernels and add WA for RDNA

Force the compiler to use all registers for gridSpreadCharge and
gridInterpolateForce by limiting max waves per EU to 1 on CDNA GPUs,
RDNA GPUs work better without it.

* Optimize atom data structs in GBSA and Amoeba on HIP

Manually rearrange fields, add paddings and force alignments to
have faster accesses to shared memory: ds_read and ds_write may
work slower if addresses are not aligned by 16 bytes.
Co-authored-by: Anton Gorenko <anton@streamhpc.com>
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

Changed format to 'pdbx' for consistency within the test framework. Added 'cif' to CMakeLists.txt for correctness for the future

fix the remaining CI issues.

Also make sure .ncrst files are copied over in the test directory.

really used CMake in-depth before).

Hopefully this fixes the Travis-CI build failures.

Install SWIG interface definition to the include directory, so outside plugins can use it when building their Python APIs

Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.