Change: more sensible default and handling of ntype

[jonathanoesterle]

• changed default ntype handling to root=-1/unknown=0 while preserving labels through all postprocessing steps. skeleton init, SWC/NPZ I/O, plotting palette, and remapping logic honor -1/0, with soma explicitly 1 when detected
• ntype remapping now aggregates labels when nodes merge (majority with a fixed priority), enforces a single root/soma, and fills zero gaps from neighboring labels.
• all node/edge-altering post ops (drop/keep, merge_near_soma_nodes, prune_neurites, detect_soma, downsample, reroot) now re-align ntype using the new remap + gap-fill; reroot also fills gaps after clearing duplicate -1/1 labels.
• visualization: SWC colormap extended to include -1 (“root”) with stable ordering.

[huangziwei]

so if we still do this, every post-processing steps will reset the existing ntype to 0.

we need to rethink how to remap ntype but preserve the existing ones.

on the other hand, in reroot, we do ntype[[0, swap]] = ntype[[swap, 0]], which is also too simple. maybe we should take edges into account also.

[jonathanoesterle]

Tested on 2 skeletons. Works for plotting, rerooting, pruning and downsampling.