refactor: split tools.ts into registry-based domain files

Replaces the single 800-line tools.ts and its switch dispatcher with a
Theia-inspired registry pattern — each tool domain is its own file, and
dispatch is a plain Map.get() call with no central routing function.

New structure in src/tools/:
  registry.ts   — ToolDefinition (with handler), registerTool(), executeTool(), ALL_TOOLS
  context.ts    — ToolContext, MemoryUpdate interfaces
  security.ts   — PROTECTED_* constants + assertGiteaWritable/assertCoolifyDeployable
  utils.ts      — safeResolve(), EXCLUDED set
  file.ts       — read_file, write_file, replace_in_file, list_directory, find_files, search_code
  shell.ts      — execute_command
  git.ts        — git_commit_and_push
  coolify.ts    — coolify_*, list_all_apps, get_app_status, deploy_app
  gitea.ts      — gitea_*, list_repos, list_all_issues, read_repo_file
  agent.ts      — spawn_agent, get_job_status
  memory.ts     — save_memory
  index.ts      — barrel with side-effect imports + re-exports

Adding a new tool now requires only a new file + registerTool() call.
No switch statement, no shared array to edit. External API unchanged.

Made-with: Cursor

dist/tools/memory.js

@@ -0,0 +1,28 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const registry_1 = require("./registry");
+(0, registry_1.registerTool)({
+    name: 'save_memory',
+    description: 'Persist an important fact about this project to long-term memory. Use this to save decisions, tech stack choices, feature descriptions, constraints, or goals so they are remembered across conversations.',
+    parameters: {
+        type: 'object',
+        properties: {
+            key: { type: 'string', description: 'Short unique label (e.g. "primary_language", "auth_strategy", "deploy_target")' },
+            type: {
+                type: 'string',
+                enum: ['tech_stack', 'decision', 'feature', 'goal', 'constraint', 'note'],
+                description: 'Category of the memory item'
+            },
+            value: { type: 'string', description: 'The fact to remember (1-3 sentences)' }
+        },
+        required: ['key', 'type', 'value']
+    },
+    async handler(args, ctx) {
+        ctx.memoryUpdates.push({
+            key: String(args.key),
+            type: String(args.type),
+            value: String(args.value)
+        });
+        return { saved: true, key: args.key, type: args.type };
+    }
+});