Update docs and tool help for package executable behavior

[t-kalinowski]

Summary

• Clarify the README and Quarto docs to use consistent project/runtime terminology and tighten the rmarkdown override guidance.
• Update tool documentation and CLI help to describe tools as supported executables in a package exec/ directory, including the distinction between Rscript/Rapp entries and direct executable scripts.
• Add platform-specific note for direct executables on Unix and Windows so users know which files are valid launch targets.
• Keep the help snapshot aligned with the revised public wording.

Notes

• The change is documentation-facing and does not alter runtime behavior.
• Internal code changes are limited to the CLI help text surfaced by ir tool --help.