refactor: move optional arguments of hrg-embedding 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 7 exported hrg-embedding 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/hrg-embedding.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
embed_adjacency_matrix()	graph, no	weights, which, scaled, cvec, options
embed_laplacian_matrix()	graph, no	weights, which, type, scaled, options
sample_sphere_surface()	dim, n	radius, positive
sample_sphere_volume()	dim, n	radius, positive
consensus_tree()	graph, hrg	start, num.samples
fit_hrg()	graph, hrg	start, steps
predict_edges()	graph, hrg	start, num.samples, num.bins

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 fb2efa0 is merged into main:

• ✔️as_adjacency_matrix: 736ms -> 738ms [-0.46%, +1.15%]
• ✔️as_biadjacency_matrix: 717ms -> 718ms [-0.67%, +0.83%]
• ✔️as_data_frame_both: 1.44ms -> 1.42ms [-3.14%, +0.47%]
• ✔️as_long_data_frame: 3.82ms -> 3.78ms [-2.49%, +0.16%]
• ✔️es_attr_filter: 2.6ms -> 2.6ms [-1.98%, +2.28%]
• ✔️graph_from_adjacency_matrix: 115ms -> 114ms [-1.83%, +0.63%]
• ✔️graph_from_data_frame: 3.24ms -> 3.24ms [-1.41%, +1.39%]
• ✔️vs_attr_filter: 1.43ms -> 1.46ms [-0.71%, +4.34%]
• ✔️vs_by_name: 930µs -> 933µs [-1.46%, +2.03%]
  Further explanation regarding interpretation and methodology can be found in the documentation.

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if e4cbbc2 is merged into main:

• ✔️as_adjacency_matrix: 800ms -> 806ms [-1.17%, +2.54%]
• ✔️as_biadjacency_matrix: 732ms -> 730ms [-1.13%, +0.59%]
• ✔️as_data_frame_both: 1.57ms -> 1.57ms [-1.79%, +1.61%]
• ✔️as_long_data_frame: 3.98ms -> 3.95ms [-2.03%, +0.73%]
• ✔️es_attr_filter: 2.84ms -> 2.81ms [-2.69%, +0.63%]
• ✔️graph_from_adjacency_matrix: 145ms -> 146ms [-1.64%, +1.83%]
• ✔️graph_from_data_frame: 3.5ms -> 3.51ms [-2.08%, +2.2%]
• ✔️vs_attr_filter: 1.58ms -> 1.58ms [-4.38%, +4.2%]
• ✔️vs_by_name: 1.02ms -> 1.03ms [-1.21%, +3.16%]
  Further explanation regarding interpretation and methodology can be found in the documentation.

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 2585709 is merged into main:

• ✔️as_adjacency_matrix: 897ms -> 892ms [-2.12%, +0.95%]
• ✔️as_biadjacency_matrix: 845ms -> 840ms [-1.9%, +0.89%]
• ✔️as_data_frame_both: 1.79ms -> 1.75ms [-5.34%, +0.13%]
• ✔️as_long_data_frame: 4.63ms -> 4.56ms [-4.35%, +1.34%]
• ✔️es_attr_filter: 3.02ms -> 2.96ms [-4.82%, +0.9%]
• ✔️graph_from_adjacency_matrix: 143ms -> 141ms [-3.39%, +0.85%]
• ✔️graph_from_data_frame: 3.83ms -> 3.8ms [-2.92%, +1.17%]
• ✔️vs_attr_filter: 1.73ms -> 1.72ms [-3.17%, +1.11%]
• 🚀vs_by_name: 1.11ms -> 1.09ms [-4.65%, -0.08%]
  Further explanation regarding interpretation and methodology can be found in the documentation.