Chaotic test implementation of many methods

[TimMonko]

• ignore notebooks and scripts
• shell of initial implementation
• add AGENTS file with project plan
• add sholl, single cell, and batch analysis
• fix ruff and add pruning
• start of directed tree analysis
• update tree for soma dilation
• properly calculate graph origin for individual skeletons
• small bump to tree format
• chaotic initial implementation

[codecov]

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