Convert internal documentation links to repository-relative paths

[Copilot]

This updates documentation links to avoid hardcoded absolute repository/site URLs for internal pages. Internal references now resolve relative to file location, while canonical external destinations remain absolute.

• Scope

  • Updated only documentation sources:
    • README.md
    • CONTRIBUTING.md

• Internal link normalization

  • Replaced absolute GitHub links to in-repo content with relative paths.
  • Examples:
    • https://github.com/FritscheLab/phewasFlow/blob/main/environment.yml → environment.yml
    • https://github.com/FritscheLab/phewasFlow/tree/main/inst/examples/slurm → inst/examples/slurm/
    • https://github.com/FritscheLab/phewasFlow#development → README.md#development

• Vignette/docs references

  • README internal “learn more” style links now target checked-in vignette sources via relative paths under vignettes/.
  • Wording was adjusted to make source-vs-rendered destinations explicit where both are referenced.

• Intentional absolutes preserved

  • Kept canonical absolute links that are not internal repository pages (e.g., GitHub issues, rendered hosted article link).

# before
[environment.yml](https://github.com/FritscheLab/phewasFlow/blob/main/environment.yml)
[README](https://github.com/FritscheLab/phewasFlow#development)

# after
[environment.yml](environment.yml)
[README](README.md#development)