v0.4.2 => v0.6.1

[IvanChernyshov]

This PR brings main from 0.4.2.post1 to 0.6.1.

This merge includes the full accumulated 0.5.x and 0.6.x line:

• 0.5.0

  • introduced the new pyvoro2.powerfit workflow
  • added reusable pair-constraint resolution, low-level fitting, realized-boundary matching, self-consistent active-set refinement, infeasibility witnesses, and report-friendly plain-Python outputs

• 0.5.1

  • hardened validation and numerical failure handling
  • added the wheel-overlay development workflow
  • refactored shared input/domain validation logic

• 0.6.0

  • added the new planar 2D namespace, pyvoro2.planar
  • introduced 2D Box / RectangularCell, compute, locate, ghost_cells, diagnostics, normalization helpers, and optional plotting
  • extended powerfit to work in both 2D and 3D
  • switched pyvoro2-authored code to LGPLv3+

• 0.6.1

  • focused on powerfit robustness and diagnostics
  • added explicit diagnostics for realized-but-unaccounted pairs
  • added candidate/active-graph connectivity diagnostics
  • improved disconnected-component gauge handling
  • added explicit weight_shift= support for weight-to-radii conversion while keeping r_min= for compatibility
  • added active-set path diagnostics so transient optimization behavior can be inspected separately from the final result

This PR also includes repository/documentation/release-workflow improvements:

• example notebooks moved to repo-root notebooks/
• generated notebook pages for docs
• notebook export/check tooling
• README/docs sync checks
• distribution-content and publishability checks
• pyvoro2[all] convenience extra
• stricter CI for docs, notebooks, and release readiness

Compatibility / scope notes:

• the 3D top-level API remains the primary public surface
• 2D support lives under pyvoro2.planar
• current planar scope covers Box and RectangularCell; generic planar PeriodicCell remains deferred
• r_min= is still accepted for backward compatibility, but weight_shift= is now the preferred explicit gauge control
• starting with 0.6.0, pyvoro2-authored code is released under LGPLv3+; vendored third-party code remains under its own licenses

This PR is intended as the release merge for 0.6.1.