(Closes #3334 #1013) Permit only module-inlined Kernels to be transformed

[arporter]

Require that all kernel transformations act only on module-inlined Kernels.
Do away with the 'rename-and-write' functionality currently used for modified kernels.
We have to keep the -okern command-line flag as that is used when creating OpenCL versions of Kernels.

[arporter]

Possibly I need to store the RoutineSymbol associated with a Kernel within the Kernel class (c.f. Call.reference). That way, I can tell whether it has been module-inlined or not and can get rid of the special flag for that.

[arporter]

Note to self: I will need to remove the kernel_outputdir test fixture.

EDIT: can't do this because we do still output OpenCL versions of kernels in some tests.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.95%. Comparing base (97543bc) to head (0949296).
⚠️ Report is 15 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3294      +/-   ##
==========================================
- Coverage   99.95%   99.95%   -0.01%     
==========================================
  Files         384      385       +1     
  Lines       54225    54087     -138     
==========================================
- Hits        54203    54065     -138     
  Misses         22       22              

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[arporter]

Coverage is now all good but the LFRic extraction integration test failed :-(

[arporter]

In lfric/eg17/full_example_extract:

$ diff main_psy.f90 on_main/main_psy.f90 
4d3
<   use testkern_w0_kernel_mod, only : testkern_w0_code
74a74
>     use testkern_w0_kernel_mod, only : some_other_var, testkern_w0_code

so it appears the some_other_var import is missing on my branch.

[arporter]

This turned out to be due to the fact that I've moved the import of Kernel routines up into the Container and then the ExtractNode was falling foul of #1734

[sergisiso]

@arporter It's good to see this (even bigger) clean up.

I just have a some questions about why some lines were changed and it may be good to have a plan for when the KernelModuleInlineTrans is made generic (see inline).

[sergisiso]

Why has this changed? I am a bit worried about this one because if the call had argument names, this would not match anymore.

[arporter]

Unfortunately, my change to ScopingNode.replace_symbols_using means that any local symbol that shadows an outer one gets replaced by the outer one. The problem I wanted to fix was where a local symbol depends on a symbol in an outer scope during a tree-copy operation. Child nodes are only attached into the new (copied) tree at the end of the copy operation - prior to that they can't see the parent scope. Therefore, only at this point can we update any references to symbols in the outer scope.