Support for Jupyter notebooks in excess of 1 MB about linguist

[lildude]

At present it appears as though linguist on GitHub handles large files (> 1MB) by reporting their byte count (or something similar) en lieu of their actual line count.

Correct. This is documented:

The percentages are calculated based on the bytes of code for each language as reported by the List Languages API.

As for:

However, when linguist is run on the full repo it reports 6677629 lines of Jupyter code.

The output is showing bytes in the second column, not lines.

As for linguist not supporting larger Jupyter files, it certainly does. If it didn't, you wouldn't get a language here and the figure in the sidebar and analysis would be significantly lower:

.../src/examples/TokaMaker/fixed_boundary/fixed_boundary_ex2.ipynb: 0 lines (0 sloc)
  type:      Text
  mime type: text/plain
  language:  Jupyter Notebook <=== ‼️ HERE
  blob is too large to be shown

The line you see below it isn't an indication of a lack of support and also doesn't apply for things like Jupyter notebooks which are rendered by a completely independent service. This information only applies to files rendered directly in GitHub's UI without any processing, like plain text python or Fortran files.

So what you are seeing is expected and correct behaviour. If you want to change this to better suit your desires, you can implement an override.