refactor: move optional arguments of conversion 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 11 exported conversion 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/conversion.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
from_adjacency()	adjmatrix	mode, weighted, diag, add.colnames, add.rownames
graph_from_adjacency_matrix()	adjmatrix	mode, weighted, diag, add.colnames, add.rownames
as_adj_edge_list()	graph	mode, loops
as_adj_list()	graph	mode, loops, multiple
as_directed()	graph	mode
as_edgelist()	graph	names
graph_from_adj_list()	adjlist	mode, duplicate
graph_from_data_frame()	d, directed	vertices
graph_from_edgelist()	el	directed
graph_from_graphnel()	graphNEL	name, weight, unlist.attrs
graph_from_biadjacency_matrix()	incidence	directed, mode, multiple, weighted, add.names

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 b2fa62d is merged into main:

• ✔️as_adjacency_matrix: 768ms -> 766ms [-1.17%, +0.52%]
• ✔️as_biadjacency_matrix: 737ms -> 741ms [-0.38%, +1.26%]
• ✔️as_data_frame_both: 1.68ms -> 1.69ms [-1.27%, +2.21%]
• ❗🐌as_long_data_frame: 4.22ms -> 4.34ms [+1.33%, +4.37%]
• ✔️es_attr_filter: 3.11ms -> 3.12ms [-2.18%, +2.81%]
• ✔️graph_from_adjacency_matrix: 117ms -> 117ms [-0.61%, +2.01%]
• ✔️graph_from_data_frame: 3.59ms -> 3.57ms [-1.64%, +0.95%]
• ✔️vs_attr_filter: 1.72ms -> 1.74ms [-0.27%, +3.58%]
• ✔️vs_by_name: 1.11ms -> 1.12ms [-1.31%, +2.53%]
  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 1afcaa5 is merged into main:

• ✔️as_adjacency_matrix: 825ms -> 824ms [-1.31%, +1.05%]
• ✔️as_biadjacency_matrix: 792ms -> 794ms [-0.87%, +1.6%]
• ✔️as_data_frame_both: 1.62ms -> 1.64ms [-1.3%, +3.5%]
• ✔️as_long_data_frame: 4.07ms -> 4.16ms [-0.11%, +4.48%]
• ✔️es_attr_filter: 2.88ms -> 2.93ms [-2.15%, +5.82%]
• ✔️graph_from_adjacency_matrix: 128ms -> 129ms [-0.63%, +2.02%]
• ✔️graph_from_data_frame: 3.53ms -> 3.57ms [-0.39%, +2.74%]
• ✔️vs_attr_filter: 1.67ms -> 1.65ms [-3.86%, +2.09%]
• ✔️vs_by_name: 1.06ms -> 1.06ms [-2.23%, +2.47%]
  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 b709507 is merged into main:

• ✔️as_adjacency_matrix: 880ms -> 881ms [-1.71%, +1.95%]
• ✔️as_biadjacency_matrix: 823ms -> 817ms [-3.11%, +1.6%]
• ❗🐌as_data_frame_both: 1.74ms -> 1.78ms [+0.65%, +4.14%]
• ✔️as_long_data_frame: 4.44ms -> 4.53ms [-2.55%, +6.74%]
• ✔️es_attr_filter: 2.8ms -> 2.79ms [-3.05%, +1.9%]
• ✔️graph_from_adjacency_matrix: 129ms -> 127ms [-3.4%, +0.84%]
• ✔️graph_from_data_frame: 3.78ms -> 3.77ms [-1.76%, +1.52%]
• ✔️vs_attr_filter: 1.63ms -> 1.63ms [-3.12%, +3.07%]
• ✔️vs_by_name: 1.01ms -> 1.01ms [-4.17%, +3.21%]
  Further explanation regarding interpretation and methodology can be found in the documentation.