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-entities/src/domain/common/store.rs

@@ -0,0 +1,63 @@
+#![allow(
+    clippy::cast_possible_truncation,
+    clippy::cast_sign_loss,
+    clippy::cast_precision_loss,
+    clippy::cast_possible_wrap
+)]
+//! Filesystem layout for zesdex's persistent and scratch data directories.
+use serde::{Deserialize, Serialize};
+use std::path::PathBuf;
+
+/// Resolved paths for all data directories zesdex reads from and writes to.
+///
+/// Why: centralizing path computation here means every consumer agrees on
+/// where memory, scratch, session images, and downloads live.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Store {
+    pub base_dir: PathBuf,
+    pub scratch_root: PathBuf,
+    pub memory_dir: PathBuf,
+    pub session_images_dir: PathBuf,
+    pub download_dir: PathBuf,
+}
+
+impl Store {
+    /// Compute the standard set of zesdex data directory paths.
+    ///
+    /// Flow: OS data dir (or `.local/share` fallback) + "zesdex" → base dir;
+    /// scratch root comes from the OS temp dir instead, since it's disposable.
+    ///
+    /// Why: paths are computed, not created — call `ensure_dirs` before use.
+    pub fn new() -> Self {
+        let base = dirs::data_dir()
+            .unwrap_or_else(|| PathBuf::from(".local/share"))
+            .join("zesdex");
+        let scratch = std::env::temp_dir().join("zesdex-scratch");
+        Store {
+            memory_dir: base.join("memory"),
+            scratch_root: scratch,
+            session_images_dir: base.join("session-images"),
+            download_dir: base.join("downloads"),
+            base_dir: base,
+        }
+    }
+
+    /// Create all store directories (base, memory, scratch, session images,
+    /// downloads) if missing.
+    ///
+    /// Return: `Err` on the first directory that fails to create.
+    pub fn ensure_dirs(&self) -> std::io::Result<()> {
+        std::fs::create_dir_all(&self.base_dir)?;
+        std::fs::create_dir_all(&self.memory_dir)?;
+        std::fs::create_dir_all(&self.scratch_root)?;
+        std::fs::create_dir_all(&self.session_images_dir)?;
+        std::fs::create_dir_all(&self.download_dir)?;
+        Ok(())
+    }
+}
+
+impl Default for Store {
+    fn default() -> Self {
+        Self::new()
+    }
+}