refactor: move optional arguments of misc 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 5 exported misc 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/misc.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
greedy_vertex_coloring()	graph	heuristic
time_bins()	x	middle
graph_from_graphdb()	url	prefix, type, nodes, pair, which, base, compressed, directed
sir()	graph, beta, gamma	no.sim
stochastic_matrix()	graph	column.wise, sparse

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 ff7ed7c is merged into main:

• ✔️as_adjacency_matrix: 580ms -> 579ms [-0.74%, +0.26%]
• ✔️as_biadjacency_matrix: 561ms -> 561ms [-0.44%, +0.6%]
• ✔️as_data_frame_both: 1.22ms -> 1.23ms [-1.34%, +2.54%]
• ✔️as_long_data_frame: 3.23ms -> 3.25ms [-0.13%, +1.07%]
• 🚀es_attr_filter: 2.32ms -> 2.29ms [-1.35%, -0.41%]
• ✔️graph_from_adjacency_matrix: 96.6ms -> 97ms [-2.9%, +3.6%]
• ✔️graph_from_data_frame: 2.75ms -> 2.75ms [-0.78%, +0.87%]
• 🚀vs_attr_filter: 1.22ms -> 1.21ms [-1.97%, -0.15%]
• ✔️vs_by_name: 777µs -> 789µs [-0.55%, +3.77%]
  Further explanation regarding interpretation and methodology can be found in the documentation.