Align Tool: atoms have to be reselected to realign to different axis

[matterhorn103]

This is with the current nightly AppImage, haven't tested with other versions yet.

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: 1.99.0
• Qt: 5.15.2

Desktop version: (please complete the following information):

• OS: openSUSE Tumbleweed with KDE Plasma 6.0.3
• Version 20240416

Describe the bug
To align a bond (or any two atoms even if not bonded) to one of the principal axes, you can select the chosen axis from the drop-down, and select two atoms in the view. Those two steps can be done in either order.

After then clicking Align, the molecules in the view are realigned appropriately. The two atoms that were selected remain selected and labelled with #1 and #2. However, changing the axis and then clicking align again doesn't result in a second realignment – the two atoms must be reselected.

To Reproduce
Steps to reproduce the behavior:

1. Draw a molecule
2. Select the Align Tool
3. Select two atoms
4. Click align (to e.g. the x-axis by default)
5. Observe successful realignment
6. Change alignment axis to e.g. z
7. Click align
8. Observe no change!
9. Reselect the same two atoms
10. Click align
11. Observe that the alignment is now successful

Expected behavior
Clicking Align should always result in realignment based on the current selection, without reselection being required.

Alternatively, all atoms should be automatically deselected after an alignment is carried out.

Both would match user expectations. The latter is less good though, as it would be convenient to be able to quickly compare the alignment to several different axes. Especially since the axes are unlabelled, meaning the user might not align to the correct axis on the first attempt.