feat(core): Add permission-controlled Deno execution, configurable script server port, improved downloader, dependency bumps and test updates

.serena/memories/suggested_commands.md

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+# Suggested Commands
+
+## Package Management
+```bash
+# Install dependencies
+pnpm install
+
+# Add runtime dependency
+pnpm install --save <package>
+
+# Add dev dependency
+pnpm install --save-dev <package>
+```
+
+## Development Commands
+
+### Building
+```bash
+# Build the project (compiles TypeScript)
+pnpm build
+# Equivalent to: tsbuild --web --allowimplicitany
+
+# Type check without building
+tsbuild check ts/**/* --skiplibcheck  # For source files
+```
+
+### Testing
+```bash
+# Run all tests
+pnpm test
+# Equivalent to: tstest test/ --web
+
+# Run specific test file
+tstest test/test.ts --verbose
+
+# Run test with log file output
+tstest test/test.ts --verbose --logfile .nogit/testlogs/test.log
+```
+
+### Documentation
+```bash
+# Build documentation
+pnpm buildDocs
+# Equivalent to: tsdoc
+```
+
+### Running TypeScript Files
+```bash
+# tsx is available globally for direct execution
+tsx path/to/file.ts
+```
+
+## Git Commands
+```bash
+# Check status
+git status
+
+# Stage and commit (use small, focused commits)
+git add <files>
+git commit -m "description"
+
+# Move files (preserves history)
+git mv old-path new-path
+```
+
+## System Commands (Linux)
+- `ls` - List directory contents
+- `cd` - Change directory
+- `grep` - Search text
+- `find` - Find files
+- `cat` - Display file contents
+- `kill <PID>` - Kill specific process (NEVER use `killall node`)
+
+## Port Management
+```bash
+# Find process on port
+lsof -i :80
+lsof -i :443
+
+# Kill specific PID
+kill <PID>
+
+# Wait between server restarts
+sleep 10
+```
+
+## Debug Scripts
+- Store debug scripts in `.nogit/debug/`
+- Run with: `tsx .nogit/debug/script-name.ts`