RProject improvements, Config Specialization, Bugfixes

[EagleoutIce]

• Configuration specialization by project kind (Support for implicit sources #2642)
  • Implicit sources: order files a framework loads on its own (global.R, ui.R, … for shiny apps), configurable
    for any project via project.implicitSources, glob-aware with typo support
• Assume sourced files exist (solver.resolveSource.assumeFilesExist): a sourced definition becomes certain, on by default for packages/projects/shiny apps
• Improved project kind identification and structure, plus better version inference
• Machine-readable linter output: format:sarif and format:github next to flowR's own summary
• Dicing gains slicing options: inlining, include-callees, magic comments,
• Full inlining (--inline-full / I, --inline-banner / B): reconstruct all files into one self-contained text in flowR's loading order
• Mermaid export hardening: ids and labels no longer break rendering
• Compact dataflow ids: _tmp_s_R-1:1-1:6-0 → s.R:1:1-0 — relative to what was requested. Cds now reads 3+ instead of :may:3+
• REPL: every code command checks for path-like input, the file protocol is prepended by default
  (repl.autoUseFileProtocol), config completion is schema-driven,
  and :query can drop its stat line (repl.queryStats) so output can be forwarded as is
• Performance: env define and cyclic Q (closes Project Query might consider a shiny app to be a package due to description? #2643), lazy CFG reverse-edge index (-18% CFG construction)
• Fixes: full lexeme for access operators, faulty pre-release R version parsing + date arbiter
• Compact plugin descriptions and a nicer plugin table in the wiki
• Various cleanup: no npm run checkup tmp dirs piling up, concentrated helpers, pruned tests, ...

[EagleoutIce]

This pull request is included in v2.13.0 (see Release v2.13.0 (Guessing Dep. Versions, Specialization, RDA)).