refactor: massive codebase restructuring — naming, splitting, DRY

Crate renames:
  - zesdex-entities::seaorm → domain (misleading name, no SeaORM used)
  - zesdex-dto → merged into zesdex-entities (100% re-exports)
  - zesdex-libs → zesdex-infra (vague name)

Module renames:
  - app/harness → guard (misleading: safety gatekeeper, not test harness)
  - runtime/commands → action_dispatch (name clashed with controller/command)
  - resources → prompts (embedded prompt text, not general resources)
  - tool/seqthink → sequential_think (unreadable abbreviation)
  - msglog/query → insert (module only inserts, never queries)

Dead code removal:
  - app/mode/help.rs (orphaned — not declared in mod.rs)
  - app/mode/loading.rs (orphaned — not declared in mod.rs)

File splitting (71 new files, avg ~115 lines/file):
  - app/runtime/actions/: 1→8 files (was 2030 lines)
  - view/overlays/: 1→16 files (was 1167 lines)
  - tool/lsp/: 1→8 per-tool files (was 909 lines)
  - main.rs: 1→5 files (session, daemon, attach, event_loop)
  - workflow/engine + hive_mind: 2→10 files
  - subagent/engine + auto: 2→9 files
  - lsp/provisioner: 1→5 files
  - review/: 1→6 files
  - guard/: 1→2 files (extracted patterns)
  - state/misc: 1→3 files (input, scroll)
  - mcp/: 1→3 files (transport, adapter)
  - stream/json_repair extracted from turn.rs

DRY:
  - Pattern constants (STUB_PATTERNS etc) in guard/patterns shared with subagent
  - 3 near-identical background spawners → 1 generic + thin wrappers
  - Shared spawn_subagent_with_drain() extracted
  - Shared create_session() in main
  - write_osc52 deduplicated

Bug fixes:
  - archive_message(): sess.db → db (wrong variable name)
  - execute_one_tool(): wrong parameter name
  - check_credential_read() function was missing (restored from test expectations)

crates/zesdex-backend/src/app/mode/help.rs

@@ -1,38 +0,0 @@
-//! Help mode: static help text and the action that opens/closes the help overlay.
-use crate::app::runtime::actions::Action;
-use crate::app::state::types::Overlay;
-
-pub const HELP_TEXT: &str = "\
-Keybindings:
-  Ctrl+C    Quit
-  Ctrl+D    Close overlay
-  Ctrl+H    Help
-  Ctrl+P    Settings
-  Ctrl+A    Toggle yolo arm
-  Ctrl+B    Bash panel
-  Ctrl+T    Todo panel
-  Ctrl+W    Workflow panel
-  Ctrl+K    Key input
-  Ctrl+L    Learning dashboard
-  Ctrl+U    Usage dashboard
-  Esc       Close overlay
-  Enter     Submit / confirm
-
-Slash commands:
-  /help             Show this help
-  /quit             Quit session
-  /mode <name>      Switch mode (chat, bash, workflow)
-  /clear            Clear transcript";
-
-/// Route an incoming action while the help overlay is open.
-///
-/// Flow: `CloseOverlay` passes through unchanged; any other action is
-/// treated as "open help" (idempotent — re-opens the overlay it's already on).
-///
-/// Return: the `Action` to actually dispatch.
-pub fn handle_help_action(action: &Action) -> Action {
-    match action {
-        Action::CloseOverlay => Action::CloseOverlay,
-        _ => Action::OpenOverlay(Overlay::Help),
-    }
-}

crates/zesdex-backend/src/app/mode/loading.rs

@@ -1,14 +0,0 @@
-//! Loading mode: transient overlay shown while waiting on an async operation.
-use crate::app::state::rest::AppStateRest;
-
-pub const LOADING_MESSAGES: &[&str] = &[
-    "processing...",
-    "thinking...",
-    "working...",
-    "almost done...",
-];
-
-/// Mark state dirty to force a re-render (e.g. to advance the loading spinner/message).
-pub fn resolve_loading(state: &mut AppStateRest) {
-    state.dirty = true;
-}