Two mechanisms, as the code has them: with -S and no reference or model, the crystals made
consistent from the data (Brehm & Diederichs objective, cell-metric anchors); with -z or --model
(-C/-S), per image against the reference, crystals their own cell decides keeping that indexing,
the data-only result as a check. Removes the statements that the ambiguity needs a reference or
model (tutorial, quick start, overview, §10.9), adds the anchoring to the reference/model rows,
the "no -S" case (mixed merge, can pass for higher symmetry, warning), and the report keys in the
reference case (AMBIGUITY_DATA_DISAGREES in place of AMBIGUITY_REINDEXED, AMBIGUITY_TIME_S,
none in --mode scale).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 8db1d3ecb97dba90471c4db238aff632d11bc3e8)
leonarski_f
6491cc5a7e
