docs: clarify planning and change detection

[kvlonge]

Why

Planning and change-detection documentation had become centred on “pruning” and --changes-only, even though direct mode no longer supports changed-only execution. That mixed the general planning contract with virtual-environment behavior and made normal direct planning harder to understand.

Changes

• rewrite the planning overview around selection, plan evidence, change reasons, cascades, incremental actions, coherence, and recorded state
• state clearly that direct mode executes its selected scope without stale filtering
• move substantive --changes-only, stale-driven execution, configuration precedence, and run_despite_unchanged guidance to Virtual Environments → Building
• distinguish direct warehouse facts from VDE-scoped state
• update source freshness, project configuration, CLI, homepage, and comparison references to match the boundary
• remove “pruning” language outside the janitor cleanup documentation

Verification

• reviewed behavior against current SQLBuild direct and virtual planners
• checked all internal Markdown routes
• git diff --check
• public-repository hygiene scan