Merged more code into common platform

[peastman]

cc @ex-rzr @philipturner

This is another step in my ongoing project to eliminate as much duplicated code as possible by putting it into the common platform. This PR replaces platform-specific implementations of two more classes with common implementations: BondedUtilities and UpdateStateDataKernel. It eliminates close to 1000 lines of duplicated code. It should allow eliminating a similar amount of code from the HIP and Metal platforms. To make the corresponding changes to them,

1. Add getAllContexts() to the ComputeContext subclass.
2. Replace the BondedUtilities subclass with a trivial stub as done for CUDA and OpenCL, or if you don't care about outside code referring to the old class just eliminate it and create a BondedUtilities directly.
3. Change the kernel factory to create a CommonUpdateStateDataKernel.

[egallicc]

@ex-rzr :

I built and successfully tested openmm-hip against openmm:master with minor modifications to support this PR. How can I ask for your review and contribute the changes to StreamHPC:develop_stream of openmm-hip? I see that PR #14 still needs to be merged by amd/openmm-hip.

(It looks like AMD is missing in action. Is there any chance we can host the HIP platform code here, @peastman? I understand that we won't be able to distribute HIP-enabled conda packages, but at least we will be able to continue support for HIP for a little bit longer. Interested users can build from sources.)

[ex-rzr]

@egallicc

Do you have a branch with your modifications? I'd like to run benchmark to check if this universal bonded force kernel is slower than the kernel from OpenMM-HIP with some additional optimizations.

[egallicc]

@ex-rzr sorry for the late reply. See https://github.com/Gallicchio-Lab/openmm-hip/tree/butil_common
Note that I wasn't looking to optimize the bonded force. The changes are simply to fix compilation errors of the develop_stream branch against the current OpenMM master branch. (Should this conversation be moved to the openmm-hip repo?) Thanks.