JIT parameterization using protobuf

[JaeseungYeom]

We already a number of options to pass to JIT module, and plain to have more.
This is a good time to make transition to protobuf based parameterization.

• Begin with src/generate_cxx_code.cpp
• Add a message schema to src/proto/wcs_params.proto
• Modify the examples under src/proto/test*
• Add a parameter structure under src/params
• Add functions to populate the structure in src/proto/wcs_paraps.cpp from user-provided prototext
• Integrate the metho into src/generate_cxx_code.cpp (look at the example in src/ssa_partition.cpp
• Apply it to src/reaction_network/network.cpp

[JaeseungYeom]

options to include

• temporary directory where the generated code are written into
• path of the library file if different from the default
  • same as the model file name except that the extension is .so under the same directory of the model file
• number of compiling threads
• whether to remove each generated source file as soon as it is used
• whether to clean up generated source files and object files
• size of each translation unit (i.e., the number of rate functions per rate formula source file)
• whether to generate the shared library if it does not already exist
• whether to save logfile for stdout and stderr
  • if so, names of the file