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/view/overlays/mod.rs

@@ -0,0 +1,126 @@
+//! Overlay rendering: each overlay variant gets its own module with a
+//! `pub fn render(frame, area, block, state)` entry point, dispatched by
+//! the top-level `render_overlay` function in this module.
+
+pub mod bash;
+pub mod clear_confirm;
+pub mod editor;
+pub mod effort;
+pub mod help;
+pub mod key_input;
+pub mod learning;
+pub mod loading;
+pub mod mcp;
+pub mod model_selector;
+pub mod quit_confirm;
+pub mod rewind;
+pub mod settings;
+pub mod todo;
+pub mod usage;
+
+use ratatui::layout::Rect;
+use ratatui::style::Style;
+use ratatui::widgets::{Block, Borders, Clear};
+use ratatui::Frame;
+use super::theme::Theme;
+
+/// Compute a centered rectangle within `area` at the given percentage width
+/// and height. The result is always at least 40 cols wide and 10 rows tall.
+pub fn centered_rect(area: Rect, percent_x: u16, percent_y: u16) -> Rect {
+    let x_pad = (area.width.saturating_sub(area.width * percent_x / 100)) / 2;
+    let y_pad = (area.height.saturating_sub(area.height * percent_y / 100)) / 2;
+
+    Rect {
+        x: area.x.saturating_add(x_pad),
+        y: area.y.saturating_add(y_pad),
+        width: area.width.saturating_sub(x_pad * 2).max(40),
+        height: area.height.saturating_sub(y_pad * 2).max(10),
+    }
+}
+
+/// Render the active modal overlay as a centered panel.
+///
+/// Each overlay gets a surface-colored panel with:
+/// - A top accent border strip (colored per variant)
+/// - A title line with icon
+/// - Content area with proper spacing
+pub fn render_overlay(
+    frame: &mut Frame,
+    area: Rect,
+    overlay: crate::app::state::types::Overlay,
+    state: &crate::app::state::rest::AppStateRest,
+) {
+    let overlay_area = centered_rect(area, 75, 70);
+
+    // Clear the area behind the overlay (semi-transparent effect)
+    frame.render_widget(Clear, overlay_area);
+
+    let block = Block::default()
+        .borders(Borders::ALL)
+        .border_style(Style::default().fg(Theme::BORDER))
+        .style(Style::default().bg(Theme::BG));
+
+    match overlay {
+        crate::app::state::types::Overlay::None => {}
+
+        crate::app::state::types::Overlay::Help => {
+            help::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Settings => {
+            settings::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Bash => {
+            bash::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::QuitConfirm => {
+            quit_confirm::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::KeyInput => {
+            key_input::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Editor => {
+            editor::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Effort => {
+            effort::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Mcp => {
+            mcp::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Todo => {
+            todo::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Rewind => {
+            rewind::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Learning => {
+            learning::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Usage => {
+            usage::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::Loading => {
+            loading::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::ModelSelector => {
+            model_selector::render(frame, overlay_area, block, state);
+        }
+
+        crate::app::state::types::Overlay::ClearConfirm => {
+            clear_confirm::render(frame, overlay_area, block, state);
+        }
+    }
+}