refactor: complete internal command bus migration

[zatevakhin]

changes

• migrate runtime, handlers, and acp client command channels from legacy protocol messages to semantic Command
• centralize load-session plus subscription ownership and remove event-loop auto-subscribe behavior
• remove the orphan App.pending_commands queue, drain path, and synthetic drain test
• keep legacy protocol helpers private/direct, including prompt wire serialization coverage
• add command pairing, prompt conversion, and load ownership regression tests

validation

• cargo fmt --all -- --check
• cargo check
• cargo clippy --all-targets -- -D warnings
• cargo build --all-targets
• cargo test --all-targets (756 passed)
• acceptance searches: zero pending_commands; no production ClientMsg outside protocol.rs; no command conversion/re-export seam; no protocol prompt type use outside protocol.rs

bounded follow-ups

• pr4 legacy cleanup removes or quarantines ClientMsg plus orphan legacy dtos and addresses the crate-wide dead_code allow; these unreferenced dto removals stay out of pr3
• mesh semantic prs 5/6 verify remote attach attached=false reconnect behavior and remote cwd when the mesh split lands; this pr does not change behavior without contract evidence
• a reconnect runtime integration sequence test is deferred because the current run_loop branch is integration-heavy; existing producer coverage verifies ordered load plus subscribe commands and session-selection coverage verifies one load and one subscribe