Require node and layer counts by name across the package

[rodvals]

Dependency

Stacked on #17. Merge after its parents, then rebase onto master and retarget.

Problem

After the previous pull request, half the package requires the dimensions to be named and half does not, and a caller has no way to remember which half. This applies one rule everywhere: a node count and a layer count are always passed by name.

Nothing unsafe changes here. A transposed call into these functions already returned the wrong length: on 4 nodes and 3 layers, compute_aggregated_multidegree(supra, 3, 4) returns 3 values where 4 are expected. The gain is consistency and the cost is a wider break, which is why it is separate and can be declined on its own. The parameters were also named n and l; since callers now have to write the names out, this is the only moment to fix that without breaking the same signatures twice.

Changes

• n and l renamed to nodes and layers in 43 functions in versatility.py, global_descriptors.py, mesoscale.py and utils/parsing.py, and both become keyword-only
• four further functions already used the right names but took them positionally, and are brought in line; three of those also had them in the reversed order
• one local list called layers renamed to layer_matrices, so the parameter name is free
• all call sites updated
• get_percolation in percolation.py, the one function I missed from the first commit

Verification

• every discovered function was called on one fixed network before and after the change. The harness can supply arguments for 49 of the 54, and all 49 return identical results; the other five need arguments it cannot guess, such as a kind string
• full suite: 750 passed, 63 skipped, against 648 and 63 on the base branch. The old seven-case test is replaced by 109 cases: one discovery check and two per function
• mypy src/: no issues found in 17 source files