Extend Mata with counter automata support

[hiraethese]

This PR extends the Mata automata library with support for GCFAs, a generalization of NFAs that includes counter guards/updates on transitions. It introduces efficient data structures, polymorphic annotation handling, and a LISP-like format for specifying automata. Core operations such as union, intersection, and membership testing are implemented for GCFAs. Benchmarks show improved performance and reduced state explosion compared to standard NFAs. This lays the foundation for advanced applications like integration with the Z3-Noodler string solver.

[codecov]

Codecov Report

❌ Patch coverage is 62.43465% with 1006 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.04%. Comparing base (c71302d) to head (6fd65d3).
⚠️ Report is 142 commits behind head on devel.

Files with missing lines	Patch %	Lines
src/cntnfa/operations.cc	66.77%	201 Missing and 93 partials ⚠️
src/cntnfa/cntnfa.cc	74.12%	75 Missing and 29 partials ⚠️
src/cntnfa/annotations.cc	13.59%	88 Missing and 1 partial ⚠️
src/cntnfa/delta.cc	78.51%	55 Missing and 29 partials ⚠️
src/cntnfa/builder.cc	61.21%	53 Missing and 30 partials ⚠️
src/cntnfa/product.cc	54.97%	53 Missing and 24 partials ⚠️
src/cntnfa/concatenation.cc	0.00%	68 Missing ⚠️
src/cntnfa/universal.cc	0.00%	66 Missing ⚠️
src/cntnfa/inclusion.cc	52.50%	45 Missing and 12 partials ⚠️
src/cntnfa/registers.cc	41.07%	31 Missing and 2 partials ⚠️
... and 8 more

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #548      +/-   ##
==========================================
- Coverage   75.88%   71.04%   -4.84%     
==========================================
  Files          43       61      +18     
  Lines        6476     9253    +2777     
  Branches     1437     2074     +637     
==========================================
+ Hits         4914     6574    +1660     
- Misses       1031     1918     +887     
- Partials      531      761     +230     

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[koniksedy]

The naming convention should be changed, especially in the builder. A lot of functions/methods operating on Cntnfa contain the word nfa instead of cntfna (Cntnfa create_single_word_nfa(...), Cntnfa construct_counter_nfa(...)...). Also, the documentation should talk about CNTNFA, not NFA, for better understandability.

[Adda0]

I agree that the naming needs to change. Primarily, Since the type of the automaton will be used repeatedly, I would opt for as the shortest name as possible. Maybe CNFA? And RNFA can then be general register NFA? So, the class name should be CNfa with this precise capitalization, and RNfa? Alternatively, Reg and Cnt are good enough, but should adhere to the naming convention, so RegNfa and CntNfa.

[Adda0]

This file should be removed.