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Document the temporal dependency problem when using kongctl and deck
together, analyze solution options (ignore/isolate flags, pending state,
two-phase plans, deck integration), and recommend Option A (explicit
ignore/isolate flags) as the initial implementation approach.

Key design decisions:
- Support both ref names and resource types in filter patterns
- Ignore mode: skip planning but keep in ResourceSet for !ref resolution
- Isolate mode: plan ONLY specified resources
- Flags are mutually exclusive
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