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/subagent/tools.rs

@@ -0,0 +1,35 @@
+//! Subagent tool filtering: maps a subagent's allowed tool names to
+//! concrete Tool trait objects and OpenAI-style tool definitions.
+//!
+//! Flow: load `all_tools()` → if `allowed_tools` is empty, use all; else
+//! filter by membership → derive `ToolDef`s for the LLM.
+
+use crate::dto::provider::request::ToolDef;
+use crate::tool::{all_tools, tool_defs};
+
+/// Build the tool list for a subagent from its allowlist.
+///
+/// An empty allowlist means "no restriction" (matches
+/// `build_subagent_context`'s default for non-reviewer roles).
+///
+/// Return: `(tool impls, schema defs)` for the subagent to use.
+pub(crate) fn build_subagent_tools(
+    allowed_tools: &[String],
+) -> (Vec<Box<dyn crate::tool::Tool>>, Vec<ToolDef>) {
+    let all = all_tools();
+    let filtered: Vec<Box<dyn crate::tool::Tool>> = if allowed_tools.is_empty() {
+        all.into_iter()
+            .filter(|t| t.name() != "hive_mind" && t.name() != "workflow_run")
+            .collect()
+    } else {
+        all.into_iter()
+            .filter(|t| {
+                allowed_tools.contains(&t.name().to_string())
+                    && t.name() != "hive_mind"
+                    && t.name() != "workflow_run"
+            })
+            .collect()
+    };
+    let defs = tool_defs(&filtered);
+    (filtered, defs)
+}