6c0b7e1 introduced a new convention for CLIs defined by Doom's modules:
to namespace them under `doom +MODULE ...`. What was once 'doom
everywhere' is now 'doom +everywhere', so the docs needed correcting.
Ref: 6c0b7e1530
Fewer links means less confusion.
- Merge doom-issue and doom-commit links into doom-ref (for auto-linking
Issue/PR/commit references).
- Merge doom-module-source and doom-docs-source links into doom-source.
- Rename doom-report-issue to doom-report.
- Use '!' as the icon for module issues link.
- Remove doom-repo (replaced with "doom:*" in :lang org module).
- Add doomdir and emacsdir links to :lang org module.