Fix light mode logo not displayed due to privacy plugin 429 errors

[Copilot]

The MkDocs privacy plugin was attempting to download logo images from GitHub URLs and hitting rate limits (429 errors), causing the light mode logo to fail rendering on github.io.

Changes

Logo references

• README.md: GitHub URLs → relative paths (docs/logo_large_*.svg) for GitHub rendering
• docs/index.md: Explicit logo tags with site-relative paths (logo_large_*.svg) for MkDocs
• docs/tutorial/cv.md: Same pattern for silhouette images

Theme-aware display

• docs/css/extra.css: Added .darkmode/.lightmode CSS rules using existing --md-logo-*-mode variables to toggle visibility based on theme

Build fix

• docs/gen_ref_nav.py: src.mosaic.__main__ → mosaic.__main__ (matches installed package structure)

Result

Light mode:

Dark mode:

No external requests for logo assets, no 429 errors.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• cdn.jsdelivr.net
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• codecov.io
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• img.shields.io
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• numpy.org
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• polyfill.io
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• static.pepy.tech
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)
• unpkg.com
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs serve --no-livereload (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean (dns block)
  • Triggering command: /usr/bin/python3 /home/REDACTED/.local/bin/mkdocs build --clean --verbose (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Light logo not displayed on github.io</issue_title>
<issue_description>Hello,

just pointing out that the logo on https://moldyn.github.io/MoSAIC/ is not displayed if I am in light mode. Happens on several devices.

Cheers :-)

</issue_description>

<agent_instructions>Please fix this issue. Running mkdocs serve works fine on the dark logo but fails on the light one with the following warning.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@braniii @taenzel thx for raising this issue. The issue seems to be that the API is limited and I am parsing too many files.

 WARNING -  Couldn't retrieve https://github.com/moldyn/MoSAIC/blob/main/docs/logo_large_light.svg?raw=true#gh-light-mode-only#gh-light-mode-only: 429 Client Error: Too Many Requests for url: https://github.com/moldyn/MoSAIC/blob/main/docs/logo_large_light.svg?raw=true#gh-light-mode-only%23gh-light-mode-only

```</body></comment_new>
</comments>

• Fixes Light logo not displayed on github.io #43

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