mistral apps capability (init, add, update, remove) now 3-way merges each generated file instead of overwriting it, so manual edits to Helm values, compose overlays, route aggregators, and apps/*/pyproject.toml survive the next wire operation. Unresolvable overlaps are written as conflict markers rather than silently discarded.
mistral apps capability merge [--continue | --abort] reconciles the generated files left in conflict by a merge.
Fixed
CLI reference docs now include the fully gated skills, prompts, and evals command groups. Root command groups are always registered and disabled ones are filtered at runtime, so the reference generator sees them.
Feature-flag docs use the real mistral_cli_ gate-key prefix and cover the ai-registry and evals disciplines; the snapshot filename, refresh budget, identity-hash contents, and ungated-command list are corrected.
