feat: graphlet_basis() returns a list of vertices in the "cliques" component. Replace .Call(Rx_...) with _impl functions for autogenerated entrypoints

[Copilot]

Replace .Call(Rx_...) with _impl functions for autogenerated entrypoints

This PR replaces manual Rx_ entrypoint implementations with calls to autogenerated _impl functions, eliminating code duplication.

Progress

• Merge main branch
• Reset and reapply changes as individual commits
• Replace Rx_ calls in cliques, interface, rewire, and foreign
• Replace Rx_ calls in cocitation, flow, and structural-properties
• Replace remaining Rx_ calls
• Remove unused Rx_ function implementations from C code

Summary

This PR completes the replacement of 38 Rx_ entrypoints with their autogenerated _impl equivalents:

Functions replaced:

• Graph structure: add_vertices, delete_edges, delete_vertices, edges, incident, ecount, is_directed
• Independent vertex sets: largest_ivs, max_ivs, ivs_size
• Graph I/O: read/write functions for pajek, graphml, gml, dl, graphdb, edgelist, dot, leda
• Flow/connectivity: mincut, mincut_value, vertex_connectivity, edge_connectivity, adhesion, cohesion
• Graph properties: constraint, coreness, topo_sort, cocitation, bibcoupling
• Other: rewire, famous, MST algorithms, graphlets, running_mean, cohesive_blocks

Removed from src/rinterface_extra.c:
All 38 now-unused Rx_ function implementations have been removed, reducing code duplication.

Not replaced:
Functions with incompatible signatures remain (e.g., maximal_cliques_count with subset, girth with circle parameter, union/intersection with list support).

Original prompt

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This section details on the original issue you should resolve

<issue_title>Replace .Call(Rx_...) with calling the corresponding _impl</issue_title>
<issue_description>For those Rx_... entrypoints where an autogenerated variant exists, use the _impl directly and remove the Rx_ implementation completely.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Replace .Call(Rx_...) with calling the corresponding _impl #2470

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[krlmlr]

Needs to remove all now unused Rx_ functions.

[krlmlr]

@copilot: Merge main . Revert to main, then add each change as an individual commit. The expectation is that the end result is identical to the state after merging main. Do not bother checking.

[Copilot]

Needs to remove all now unused Rx_ functions.

Done in ddbb826. Removed 38 unused Rx_ function implementations from src/rinterface_extra.c.

@copilot: Merge main . Revert to main, then add each change as an individual commit. The expectation is that the end result is identical to the state after merging main. Do not bother checking.

Done. Merged main, reset to main, then reapplied changes as individual commits:

• 64fb71c: Replace Rx_ calls in cliques, interface, rewire, and foreign
• ec211e2: Replace Rx_ calls in cocitation, flow, and structural-properties
• 3bdbc77: Replace remaining Rx_ calls
• ddbb826: Remove unused Rx_ implementations from C code