docs(revdep): Add reprexes for bootcluster, checked, htna and SEMdeep

[krlmlr]

The four packages revdep2 run 31048405399 flagged that the committed revdep/ report does not. Each gets the two files this directory uses -- a runnable script and the reprex output -- and they turn out to be four different stories:

• bootcluster calls sample_degseq(method = "simple.no.multiple") from scheme2.exp(). Defunct since 2.1.0, same as qgraph and degreenet. Still errors on 2.3.3.9029. CRAN lists no URL or BugReports for it, so it is an email to the maintainer.
• checked passes mode positionally to neighbors(). That is soft-deprecated for 3.0.0 and only warns -- but the package's tests are snapshot tests, so 315 warnings become one failure. A one-word fix upstream.
• htna cascades through tna:::as.igraph.matrix(), whose call to graph_from_adjacency_matrix() ends in a trailing comma. That empty argument used to reach the migration handler and error; it does not any more, so the reproducer passes and is kept as a regression test rather than sent anywhere.
• SEMdeep fails inside SEMgraph::SEMrun() with a subscript out of bounds and no igraph function on the backtrace -- a silent result change, the same shape as SEMgraph's own open item. It is the one example here that is neither reduced nor rendered: SEMgraph needs Bioconductor packages that do not install where the others were rendered, so its .md carries the check log and a list of what to compare instead.

Rendered with reprex against a locally built igraph 2.3.3.9029, so the outputs are what the current development version actually does.

Claude-Session: https://claude.ai/code/session_01DdNk5vJPSUidKGdnAYt7Dv

• By submitting this pull request, I assign the copyright of my contribution to The igraph development team.

[krlmlr]

Fold into #2646.