chore: Configure pre-commit, update the justfile

[aborgna-q]

Setups pre-commit instead of the ad-hoc .github/pre-commit file, and cleans up the just recipes.

The main benefit of this is to avoid running both codebase tests on each commit, since pre-commit filters the required checks based on the modified files.

Updates DEVELOPMENT.md with the new commands. It should be a bit more straightforward now.

drive-by: Fixes for the trailing-whitespace and end-of-file-fixer hooks.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.55%. Comparing base (3406e88) to head (d82d695).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #890      +/-   ##
==========================================
- Coverage   85.62%   85.55%   -0.07%     
==========================================
  Files          78       78              
  Lines       14397    14396       -1     
  Branches    14397    14396       -1     
==========================================
- Hits        12327    12317      -10     
- Misses       1436     1445       +9     
  Partials      634      634              

Flag	Coverage Δ
python	∅ <ø> (∅)
rust	85.55% <ø> (-0.07%)	⬇️

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[cqc-alec]

I ran just check on this branch and got a couple of errors:

(env) alec:~/r/hugr$ just check
poetry run pre-commit run --all-files
[INFO] Initializing environment for https://github.com/astral-sh/ruff-pre-commit.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy:pydantic.
[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check for added large files..............................................Passed
check for case conflicts.................................................Passed
check that executables have shebangs.....................................Failed
- hook id: check-executables-have-shebangs
- exit code: 1

specification/schema/serialization.md: marked executable but has no (or invalid) shebang!
  If it isn't supposed to be executable, try: `chmod -x specification/schema/serialization.md`
  If on Windows, you may also need to: `git add --chmod=-x specification/schema/serialization.md`
  If it is supposed to be executable, double-check its shebang.

check for merge conflicts................................................Passed
check toml...............................................................Passed
check vcs permalinks.....................................................Passed
check yaml...............................................................Passed
detect private key.......................................................Passed
fix end of files.........................................................Failed
- hook id: end-of-file-fixer
- exit code: 1
- files were modified by this hook

Fixing specification/schema/hugr_schema_v1.json
Fixing specification/schema/hugr_schema_v0.json

trim trailing whitespace.................................................Passed
fix utf-8 byte order marker..............................................Passed
mixed line ending........................................................Passed
check python ast.........................................................Passed
check docstring is first.................................................Passed
debug statements (python)................................................Passed
ruff.....................................................................Passed
ruff-format..............................................................Passed
mypy.....................................................................Passed
cargo format.............................................................Passed
cargo check..............................................................Passed
cargo test...............................................................Passed
cargo clippy.............................................................Passed
error: Recipe `check` failed on line 13 with exit code 1

Should we fix these before merging?

[aborgna-q]

Done.
It may be problematic that we have extra tests here that are not ran in CI (end-of-file-fixer and trailing-whitespace are the most problematic).
Should I disable them?

[cqc-alec]

Happy to keep or disable those checks.

[aborgna-q]

Let's leave them for now, we can always disable them if they become annoying