feat: colour filaments by object, and filament transparency

[uermel]

Filament tubes were always coloured by filament ID, and could not be made transparent.

New

• copick filament style [color instance|object] [transparency PERCENT] colours all filament sets by filament ID or by their object's colour, and sets the tubes' transparency. Without options it reports the current style.
• The Copick Annotate window's Filaments page gets the same controls: a "Colour by instance" checkbox above the filament list, and a "Transparency" box. In object mode the list swatches show the object's colour too.

Behaviour

• Instance colours take their alpha from the object's colour, so a given transparency looks the same in both modes.
• The transparency reduces the alpha of the object's colour, so a config alpha below 255 still counts. 0 keeps it; 100 hides the tubes.
• Both settings are saved in the ChimeraX settings (filament_color_by_instance, filament_transparency) and apply to every open set immediately, without rebuilding tubes.
• Control points stay opaque, so editing stays readable.
• The filament command help documents it, and its shortcut line now lists cf and jf as well.

Tested in ChimeraX 1.12

• object mode at 50 %: tube = object colour with alpha 128;
• instance mode: distinct instance colours, all with alpha 128;
• applies to every open set;
• handles stay opaque;
• the setting persists;
• the panel shows 50 % and the checkbox state.

Unit tests and the CI lint steps pass on both lines.

🤖 Generated with Claude Code