epam / miew / 29377072750

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Add a setting to switch auto-bonding off (#615)

Add a global `autoBonding` setting ('default'|'disable'|'force') that
controls whether bonds are automatically reconstructed on load,
independent of file format. A per-load override is available via
`opts.autoBonding` on `Miew#load()`, taking precedence over the global
setting.

- Add `Parser#resolveAutoBonding()` to resolve the per-load override,
  global setting, and per-format default, in that order of precedence.
- Wire it into PDB, CIF, GRO, XYZ, SDF, MOL2, CML, MMTF, and PubChem
  parsers, replacing their hardcoded `needAutoBonding` flags.
- Document `opts.autoBonding` on `Miew#load()`.
- Add tests for `resolveAutoBonding()` and the new setting default.

nohetatm mode is deferred to a follow-up issue.

Co-authored-by: GitHub Copilot <copilot@github.com>

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