Clean up old version usages and SPEC0 pin a few more deps

[larsoner]

I used Claude Opus 5 to look for places we had cruft / technical debt from old versions, and places that we should have TODO VERSION and don't. It found a lot, including a bug regarding buttons:

from pathlib import Path

import mne

mne.viz.set_browser_backend("matplotlib")
fname = Path(mne.__file__).parent / "io" / "tests" / "data" / "test_raw.fif"
raw = mne.io.read_raw_fif(fname, verbose="error").crop(0, 5).pick("mag")
fig = raw.plot(group_by="selection", block=True)

buttons = fig.mne.fig_selection.mne.radio_ax.buttons
print(buttons.ax.collections[0].get_facecolor())

Click the Channel selection window and press b: on this branch every radio button fills in; on main only the active one does.

Also moves a few packages into SPEC0-checking (nilearn, dipy, nibabel, mne-qt-browser, numba) as it allows us to remove some old code / checks. And includes a tiny fix that hopefully helps CircleCI when there are apt downloading issues.

Opus drafted the changes but I iterated until I was happy with them.

[drammock]

since this script is migrating to mne-tools repo soon, let's make sure these changes make it there too. cc @tsbinns