refactor(core): split agent/mod.rs monolith into focused submodules

[bug-ops]

Summary

crates/zeph-core/src/agent/mod.rs held a single impl<C: Channel> Agent<C> block of 58 methods across 4120 lines — the largest production monolith in the workspace. This splits it into focused submodules along concern boundaries, following the pattern of the prior agent/persistence (#4878), router (#4875), and config (#4874) splits.

mod.rs is reduced to ~2000 lines, retaining only the struct definition, DispatchFlow, constructors, the main agent loop (run and its dispatch helpers), and the free helper functions used by the loop.

Extracted submodules

File	Responsibility
shutdown.rs	Graceful shutdown: structured session-summary generation (with plain-text fallback) + orphaned tool-use tombstone flush
subagent_commands.rs	/agent command handlers (list/status/approve/deny/spawn/cancel/resume), sub-agent polling, and bounded spawn-context assembly (incl. the estimate_parts_size / trim_parent_messages / sanitize_parent_messages helpers)
skill_reload.rs	Skill matcher rebuild, trust refresh, and skill/instruction hot-reload
config_reload.rs	Config overlay hot-reload, context-budget recompute, shell-overlay divergence warning
hooks_dispatch.rs	CwdChanged / FileChanged lifecycle hook dispatch + the McpManagerDispatch MCP-bridge adapter

The three SideQuest eviction methods (maybe_sidequest_eviction, sidequest_apply_pending, sidequest_schedule_next) move into the existing sidequest.rs.

Visibility

The shared impl block is now split across files. Because a private inherent method defined in agent::<submodule> is no longer visible to the parent agent module or its siblings, the 14 methods called cross-module are bumped to pub(super); every method called only within its own new module stays private. No public API change — pub / pub(crate) signatures are untouched.

The one internal test referencing the moved crate::agent::{estimate_parts_size, trim_parent_messages} free functions is updated to the new subagent_commands path. The stale do-not-split TODO at the top of mod.rs (which predated and is superseded by this work) is removed.

Validation

• cargo +nightly fmt --check — clean
• cargo clippy --workspace --all-targets -- -D warnings — clean
• RUSTFLAGS="-D warnings" cargo check --workspace --all-targets --features desktop,ide,server,chat,pdf,scheduler --locked — clean
• cargo nextest run --workspace --lib --bins — 10530 passed, 21 skipped
• cargo test --doc -p zeph-core — 32 passed
• RUSTDOCFLAGS="--deny rustdoc::broken_intra_doc_links" cargo doc --no-deps -p zeph-core — builds (one pre-existing unrelated warning in builder.rs)

Closes #4923