refactor: move optional arguments of topology functions behind the ellipsis

[krlmlr]

Part of the repo-wide ellipsis migration coordinated in #2757 —
see that PR for the full rationale (CONTRIBUTING.md, Argument Order and the Ellipsis).
Based directly on main (the registry split landed via #2779); a single topic commit.

What this does

Inserts ... between the defining arguments (head) and the optional
modifiers (tail) of 10 exported topology functions.
Arguments after ... become keyword-only.

• Legacy positional or abbreviated calls are recovered by the generated
  ARG_HANDLE block and emit a single lifecycle::deprecate_soft("3.0.0", …) —
  behavior is unchanged.
• No defaults change, no arguments are renamed, deprecated functions untouched.
• Registry: tools/migrations/topology.R; blocks regenerated via
  Rscript tools/generate-migrations.R (idempotent, CI-checked).
• Rd usage/arguments updated mechanically (see note below).

New signatures

function	head (positional)	keyword-only tail
automorphism_group()	graph, colors	sh, details
canonical_permutation()	graph, colors	sh
count_automorphisms()	graph, colors	sh
graph.count.isomorphisms.vf2()	graph1, graph2	vertex.color1, vertex.color2, edge.color1, edge.color2
graph.count.subisomorphisms.vf2()	graph1, graph2	vertex.color1, vertex.color2, edge.color1, edge.color2
graph.isomorphic.bliss()	graph1, graph2	colors1, colors2, sh
graph.isomorphic.vf2()	graph1, graph2	vertex.color1, vertex.color2, edge.color1, edge.color2
graph.subisomorphic.lad()	pattern, target	domains, induced, map, all.maps, time.limit
graph.subisomorphic.vf2()	graph1, graph2	vertex.color1, vertex.color2, edge.color1, edge.color2
graph_from_isomorphism_class()	size, number	directed

Notes for review

• The environment used to prepare this PR cannot install igraph.r2cdocs
  (GitHub API unreachable), so man/*.Rd files were updated mechanically
  (usage + ... argument item) instead of via devtools::document().
  R CMD check's usage↔formals validation passes; a follow-up
  devtools::document() run may reflow whitespace but should produce no
  semantic diff.
• Package tests that called these functions positionally were updated to
  named arguments (they are the same soft-deprecation user code will see).

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 2c90e23 is merged into main:

• ✔️as_adjacency_matrix: 765ms -> 761ms [-1.18%, +0.15%]
• ✔️as_biadjacency_matrix: 729ms -> 727ms [-1.05%, +0.46%]
• ✔️as_data_frame_both: 1.67ms -> 1.66ms [-1.84%, +0.99%]
• ✔️as_long_data_frame: 4.28ms -> 4.3ms [-1.39%, +2.03%]
• ✔️es_attr_filter: 2.97ms -> 2.94ms [-3.31%, +1.24%]
• ✔️graph_from_adjacency_matrix: 117ms -> 116ms [-1.05%, +0.75%]
• ✔️graph_from_data_frame: 3.51ms -> 3.49ms [-2.62%, +1.7%]
• ✔️vs_attr_filter: 1.64ms -> 1.66ms [-1.22%, +2.84%]
• ✔️vs_by_name: 1.05ms -> 1.05ms [-2.19%, +2.71%]
  Further explanation regarding interpretation and methodology can be found in the documentation.