Inline Tools class into KMIR and replumb

[ehildenb]

In preparation of building LHSs of specs directly, I've inlined the Tools class directly into the KMIR class, and propagated all the appropriate changes through.

This also required getting KParse to match the diamond import pattern of KRun and KProve (which I think is eventually the intention, to upstream it), so I did that as well.

Overall, this moves make_init_config and run_parsed directly into KMIR, so it's available for all commands that KMIR exposes.

As one minor build system improvement, I allow the user to set variable PARALLEL on the CLI when invoking make to spede things up.

[ehildenb]

Need to check that both versions of the tests (llvm and haskell) are being run for test_exec_smir.

[jberthold]

Nice clean-up!