Move and rename the include directory to sharedlib

[rs028]

This is the final step in reorganizing the model/ directory. The new structure is:

• configuration : the configuration directory, set by build script flag --configuration=. Includes the *.config and *.parameters files, plus customRateFuncs.f90. These files are editable by the user.
• constraints : the constraints directory (not changed)
• output : the output directory (not changed)
• sharedlib : the shared library directory, set by build script flag --shared_lib= . Includes the auto-generated mechanism.* files and the pre-compiled mechanism shared library (mechanism.so). These files should not be editable by the user.
• mechanism.fac : the chemical mechanism file, set by build script flag --mechanism=, During build, this is converted in the mechanism.* files and compiled together with customRateFuncs.f90 into the mechanism shared library.

Other changes:

• the build script flag --mcm= is repurposed to indicate the version of the MCM files
• the executable does not have a --mcm= flag anymore
• the executable flag --shared_lib does not point to the mechanism.so file, but to the directory where the file is located (i.e. model/sharedlib

@AlfredMayhew @bsn502, any comments?

[codecov]

Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 51.73%. Comparing base (c4ed6af) to head (45372fb).
⚠️ Report is 34 commits behind head on master.

Files with missing lines	Patch %	Lines
src/argparse.f90	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #548      +/-   ##
==========================================
- Coverage   52.05%   51.73%   -0.32%     
==========================================
  Files          17       17              
  Lines        2096     2101       +5     
  Branches      166      167       +1     
==========================================
- Hits         1091     1087       -4     
- Misses        933      942       +9     
  Partials       72       72              

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[AlfredMayhew]

I've had a quick go at running this and it seems to work as you describe. The only point I have might be related to something I have raised before, so apologies if I'm repeating myself.

It would be nice to not have to specify the --mechanism flag for the build script, as was the old behaviour. If you just pass a single argument, it was automatically read as the mechanism path. Currently not specifying the --mechanism flag raises this error: [INPUT ERROR] The chemical mechanism file (.fac/.kpp) must be provided. . Having to specify the flag name prevents tab completion of the path (at least for my setup), so it actually results in quite a bit of extra typing for each build.

Apart from that, all seems good to me.

[rs028]

@AlfredMayhew I think this may be related to the way your shell is setup. Anyways it should now work as you suggest (although I haven't tested it fully). You still have to specify the flags for the other directories if you don't use the default values, though. If this is okay you can approve the PR, otherwise let's talk what other modifications are needed.

[AlfredMayhew]

I think you're right about the tab completion being to do with my set-up. I'm running with Windows Subsystem for Linux, so it get's a bit weird sometimes.
I've given this a quick go and it seems to work as expected. Thanks!