feat: toggle optimize topology-cleanup steps - #948
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Gate the per-iteration topology cleanup with --no-collapse-short-branches, --no-merge-siblings, and --no-flip-parent-child. Each defaults on, so an optimize run with no topology flags is unchanged. The switches are carried through OptimizeParams as a TopologyOps struct. Merge and flip-parent-child require the sparse representation, so they warn when disabled under --dense where they cannot run.
Regenerated from the current CLI. The generator emits the whole reference document, so this also refreshes command entries that were left stale on the base branch.
ivan-aksamentov
changed the title
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feat/optimize-polytomy-reversion-resolution
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rust
September 3, 2026 06:28
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Update:
kb/features/optimize.md: record the per-step topology toggles
Depends on: feat: resolve reversion-driven polytomies in the optimize loop #947
The three topology-cleanup steps (collapse, merge, hoist) ran unconditionally. This adds
--no-collapse-short-branches,--no-merge-siblings, and--no-flip-parent-childto disable each step independently. All default on.Work items
TopologyOpscarrying the three switches, all defaulting on [src]