refactor: reorganize crate structure and split large modules (#536)

- Move all crates from root directories to src/ for centralized organization
- Split large modules (>500 lines) into logical submodules for better maintainability
- Refactored modules across multiple crates:
  - cortex-cli: split command modules (agent, dag, debug, mcp, scrape)
  - cortex-engine: split session, auth, commands, hooks, store, registry, edit_strategies
  - cortex-tui: split app, sessions, handlers, form, executor, actions, command_palette
  - cortex-core: split spinner, renderer, animation
  - cortex-gui: split formatter, settings, extensions, lsp, testing, dap modules
  - cortex-storage: split sessions module
  - cortex-mcp-server: split lib.rs into submodules
  - cortex-mcp-types: split lib.rs into submodules
  - cortex-execpolicy: split lib.rs into submodules
  - cortex-login: split lib.rs into submodules
  - cortex-app-server: split api and tools modules
  - cortex-protocol: split protocol module
  - cortex-plugins: split hooks module
  - cortex-common: split model_presets module
  - cortex-lsp: split client and downloader modules
  - cortex-compact: split auto_compaction module
- Split utility modules (fs, git, remote, mcp-manager)
- Fix security module exports and rename DoomLoopDetector
- Implement cortex-utils-pty module with proper exports
- Replace hardcoded values and TODO comments with proper documentation
- Update include_str paths for relocated files

Author: echobt

Cargo.toml

@@ -4,93 +4,93 @@ members = [
     # ==========================================================================
     # CLI Application
     # ==========================================================================
-    "cortex-cli",
-    "cortex-engine",
-    "cortex-protocol",
-    "cortex-exec",
+    "src/cortex-cli",
+    "src/cortex-engine",
+    "src/cortex-protocol",
+    "src/cortex-exec",
 
     # CLI - Security
-    "cortex-execpolicy",
-    "cortex-sandbox",
-    "cortex-process-hardening",
-    "cortex-linux-sandbox",
-    "cortex-windows-sandbox",
+    "src/cortex-execpolicy",
+    "src/cortex-sandbox",
+    "src/cortex-process-hardening",
+    "src/cortex-linux-sandbox",
+    "src/cortex-windows-sandbox",
 
     # CLI - MCP
-    "cortex-mcp-server",
-    "cortex-mcp-types",
-    "cortex-mcp-client",
+    "src/cortex-mcp-server",
+    "src/cortex-mcp-types",
+    "src/cortex-mcp-client",
 
     # CLI - Tools
-    "cortex-apply-patch",
-    "cortex-file-search",
-    "cortex-common",
+    "src/cortex-apply-patch",
+    "src/cortex-file-search",
+    "src/cortex-common",
 
     # CLI - Storage
-    "cortex-storage",
+    "src/cortex-storage",
 
     # CLI - Authentication
-    "cortex-login",
-    "cortex-keyring-store",
+    "src/cortex-login",
+    "src/cortex-keyring-store",
 
     # CLI - Feedback & Telemetry
-    "cortex-feedback",
-    "cortex-otel",
+    "src/cortex-feedback",
+    "src/cortex-otel",
 
     # CLI - Server
-    "cortex-app-server",
+    "src/cortex-app-server",
 
     # CLI - Utilities
-    "cortex-utils/git",
-    "cortex-utils/pty",
-    "cortex-utils/image",
-    "cortex-utils/string",
-    "cortex-utils/cache",
-    "cortex-utils/file-safety",
+    "src/cortex-utils/git",
+    "src/cortex-utils/pty",
+    "src/cortex-utils/image",
+    "src/cortex-utils/string",
+    "src/cortex-utils/cache",
+    "src/cortex-utils/file-safety",
 
     # CLI - Features (Phase 1)
-    "cortex-lsp",
-    "cortex-snapshot",
-    "cortex-agents",
-    "cortex-hooks",
-    "cortex-share",
-    "cortex-plugins",
-    "cortex-batch",
+    "src/cortex-lsp",
+    "src/cortex-snapshot",
+    "src/cortex-agents",
+    "src/cortex-hooks",
+    "src/cortex-share",
+    "src/cortex-plugins",
+    "src/cortex-batch",
 
     # CLI - Features (Phase 2)
-    "cortex-ghost",
-    "cortex-review",
-    "cortex-resume",
-    "cortex-compact",
-    "cortex-ratelimits",
-    "cortex-migrations",
-    "cortex-experimental",
-    "cortex-commands",
-    "cortex-skills",
-    "cortex-prompt-harness",
+    "src/cortex-ghost",
+    "src/cortex-review",
+    "src/cortex-resume",
+    "src/cortex-compact",
+    "src/cortex-ratelimits",
+    "src/cortex-migrations",
+    "src/cortex-experimental",
+    "src/cortex-commands",
+    "src/cortex-skills",
+    "src/cortex-prompt-harness",
 
     # CLI - Features (Phase 3 - Codex-inspired)
-    "cortex-collab",
-    "cortex-network-proxy",
-    "cortex-shell-snapshot",
+    "src/cortex-collab",
+    "src/cortex-network-proxy",
+    "src/cortex-shell-snapshot",
 
     # CLI - Integrations
-    "cortex-slack",
+    "src/cortex-slack",
 
     # CLI - LM Studio Integration
-    "cortex-lmstudio",
+    "src/cortex-lmstudio",
 
     # CLI - Ollama Integration
-    "cortex-ollama",
+    "src/cortex-ollama",
 
     # CLI - TUI
-    "cortex-core",
-    "cortex-tui",
-    "cortex-tui-capture",
-    "cortex-tui-components",
+    "src/cortex-core",
+    "src/cortex-tui",
+    "src/cortex-tui-capture",
+    "src/cortex-tui-components",
 
     # CLI - Auto-Update
-    "cortex-update",
+    "src/cortex-update",
 
     # CLI - OpenTUI Framework
     "opentui-rs",
@@ -106,7 +106,7 @@ members = [
     # ==========================================================================
     # Desktop Application (GUI) - Tauri
     # ==========================================================================
-    "cortex-gui/src-tauri",
+    "src/cortex-gui/src-tauri",
 ]
 
 [workspace.package]
@@ -176,65 +176,65 @@ once_cell = "1.19"
 # ==========================================================================
 
 # CLI internal crates
-cortex-cli = { path = "cortex-cli" }
-cortex-engine = { path = "cortex-engine" }
-cortex-protocol = { path = "cortex-protocol" }
-cortex-exec = { path = "cortex-exec" }
-cortex-execpolicy = { path = "cortex-execpolicy" }
-cortex-sandbox = { path = "cortex-sandbox" }
-cortex-mcp-server = { path = "cortex-mcp-server" }
-cortex-mcp-types = { path = "cortex-mcp-types" }
-cortex-mcp-client = { path = "cortex-mcp-client" }
-cortex-apply-patch = { path = "cortex-apply-patch" }
-cortex-file-search = { path = "cortex-file-search" }
-cortex-common = { path = "cortex-common" }
-cortex-utils-git = { path = "cortex-utils/git" }
-cortex-utils-pty = { path = "cortex-utils/pty" }
-cortex-utils-image = { path = "cortex-utils/image" }
-cortex-utils-string = { path = "cortex-utils/string" }
-cortex-utils-cache = { path = "cortex-utils/cache" }
-cortex-utils-file-safety = { path = "cortex-utils/file-safety" }
-cortex-login = { path = "cortex-login" }
-cortex-keyring-store = { path = "cortex-keyring-store" }
-cortex-feedback = { path = "cortex-feedback" }
-cortex-otel = { path = "cortex-otel" }
-cortex-process-hardening = { path = "cortex-process-hardening" }
-cortex-app-server = { path = "cortex-app-server" }
-cortex-commands = { path = "cortex-commands" }
-cortex-storage = { path = "cortex-storage" }
-cortex-core = { path = "cortex-core" }
-cortex-tui = { path = "cortex-tui" }
-cortex-tui-capture = { path = "cortex-tui-capture" }
-cortex-tui-components = { path = "cortex-tui-components" }
-cortex-update = { path = "cortex-update" }
-cortex-lsp = { path = "cortex-lsp" }
-cortex-snapshot = { path = "cortex-snapshot" }
-cortex-agents = { path = "cortex-agents" }
-cortex-hooks = { path = "cortex-hooks" }
-cortex-share = { path = "cortex-share" }
-cortex-plugins = { path = "cortex-plugins" }
-cortex-batch = { path = "cortex-batch" }
-cortex-ghost = { path = "cortex-ghost" }
-cortex-review = { path = "cortex-review" }
-cortex-resume = { path = "cortex-resume" }
-cortex-compact = { path = "cortex-compact" }
-cortex-ratelimits = { path = "cortex-ratelimits" }
-cortex-migrations = { path = "cortex-migrations" }
-cortex-experimental = { path = "cortex-experimental" }
-cortex-linux-sandbox = { path = "cortex-linux-sandbox" }
-cortex-windows-sandbox = { path = "cortex-windows-sandbox" }
-cortex-lmstudio = { path = "cortex-lmstudio" }
-cortex-ollama = { path = "cortex-ollama" }
-cortex-skills = { path = "cortex-skills" }
-cortex-prompt-harness = { path = "cortex-prompt-harness" }
+cortex-cli = { path = "src/cortex-cli" }
+cortex-engine = { path = "src/cortex-engine" }
+cortex-protocol = { path = "src/cortex-protocol" }
+cortex-exec = { path = "src/cortex-exec" }
+cortex-execpolicy = { path = "src/cortex-execpolicy" }
+cortex-sandbox = { path = "src/cortex-sandbox" }
+cortex-mcp-server = { path = "src/cortex-mcp-server" }
+cortex-mcp-types = { path = "src/cortex-mcp-types" }
+cortex-mcp-client = { path = "src/cortex-mcp-client" }
+cortex-apply-patch = { path = "src/cortex-apply-patch" }
+cortex-file-search = { path = "src/cortex-file-search" }
+cortex-common = { path = "src/cortex-common" }
+cortex-utils-git = { path = "src/cortex-utils/git" }
+cortex-utils-pty = { path = "src/cortex-utils/pty" }
+cortex-utils-image = { path = "src/cortex-utils/image" }
+cortex-utils-string = { path = "src/cortex-utils/string" }
+cortex-utils-cache = { path = "src/cortex-utils/cache" }
+cortex-utils-file-safety = { path = "src/cortex-utils/file-safety" }
+cortex-login = { path = "src/cortex-login" }
+cortex-keyring-store = { path = "src/cortex-keyring-store" }
+cortex-feedback = { path = "src/cortex-feedback" }
+cortex-otel = { path = "src/cortex-otel" }
+cortex-process-hardening = { path = "src/cortex-process-hardening" }
+cortex-app-server = { path = "src/cortex-app-server" }
+cortex-commands = { path = "src/cortex-commands" }
+cortex-storage = { path = "src/cortex-storage" }
+cortex-core = { path = "src/cortex-core" }
+cortex-tui = { path = "src/cortex-tui" }
+cortex-tui-capture = { path = "src/cortex-tui-capture" }
+cortex-tui-components = { path = "src/cortex-tui-components" }
+cortex-update = { path = "src/cortex-update" }
+cortex-lsp = { path = "src/cortex-lsp" }
+cortex-snapshot = { path = "src/cortex-snapshot" }
+cortex-agents = { path = "src/cortex-agents" }
+cortex-hooks = { path = "src/cortex-hooks" }
+cortex-share = { path = "src/cortex-share" }
+cortex-plugins = { path = "src/cortex-plugins" }
+cortex-batch = { path = "src/cortex-batch" }
+cortex-ghost = { path = "src/cortex-ghost" }
+cortex-review = { path = "src/cortex-review" }
+cortex-resume = { path = "src/cortex-resume" }
+cortex-compact = { path = "src/cortex-compact" }
+cortex-ratelimits = { path = "src/cortex-ratelimits" }
+cortex-migrations = { path = "src/cortex-migrations" }
+cortex-experimental = { path = "src/cortex-experimental" }
+cortex-linux-sandbox = { path = "src/cortex-linux-sandbox" }
+cortex-windows-sandbox = { path = "src/cortex-windows-sandbox" }
+cortex-lmstudio = { path = "src/cortex-lmstudio" }
+cortex-ollama = { path = "src/cortex-ollama" }
+cortex-skills = { path = "src/cortex-skills" }
+cortex-prompt-harness = { path = "src/cortex-prompt-harness" }
 
 # Phase 3 - Codex-inspired crates
-cortex-collab = { path = "cortex-collab" }
-cortex-network-proxy = { path = "cortex-network-proxy" }
-cortex-shell-snapshot = { path = "cortex-shell-snapshot" }
+cortex-collab = { path = "src/cortex-collab" }
+cortex-network-proxy = { path = "src/cortex-network-proxy" }
+cortex-shell-snapshot = { path = "src/cortex-shell-snapshot" }
 
 # Integrations
-cortex-slack = { path = "cortex-slack" }
+cortex-slack = { path = "src/cortex-slack" }
 
 # OpenTUI crates
 opentui = { path = "opentui-rs" }