fix(appdata): Fix iteration over overwriteObject in AppData and update configuration for dependency and path handling

.serena/memories/coding_standards.md

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+# Coding Standards for npmextra
+
+## Naming Conventions
+- **Interfaces**: Prefix with `I` (e.g., `IAppDataOptions`, `ITestOptions`)
+- **Types**: Prefix with `T` (e.g., `TKeyValueStore`)
+- **Filenames**: Always lowercase (e.g., `npmextra.classes.appdata.ts`)
+- **Module structure**: `npmextra.<type>.<name>.ts` pattern
+
+## Import/Export Patterns
+- Use ES module syntax (`import`/`export`)
+- Import all dependencies through `npmextra.plugins.ts`
+- Reference with full path: `plugins.moduleName.className()`
+- Export all public APIs through `index.ts`
+
+## TypeScript Patterns
+- Use generic types for flexibility (`<T = any>`)
+- Leverage TypeScript utility types from `@tsclass/tsclass`
+- Use async/await for asynchronous operations
+- Use Promises with smartpromise utilities
+
+## Testing Standards
+- Import expect from `@git.zone/tstest/tapbundle`
+- Test files end with `export default tap.start()`
+- Use descriptive test names with `tap.test()`
+- Test file naming: `test.*.ts` pattern
+
+## Code Quality
+- Make focused, goal-oriented changes
+- Preserve necessary complexity
+- Remove redundancy carefully
+- Keep async patterns where they add value
+- No comments unless explicitly requested

.serena/memories/project_overview.md

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+# npmextra Project Overview
+
+## Purpose
+npmextra is a utility library that enhances npm with additional configuration and tool management capabilities. It provides a key-value store for project setups and centralized configuration management through npmextra.json files.
+
+## Tech Stack
+- TypeScript (ES modules)
+- Node.js
+- Dependencies:
+  - @push.rocks/qenv - Environment variable management
+  - @push.rocks/smartfile - File system operations
+  - @push.rocks/smartjson - JSON handling
+  - @push.rocks/smartlog - Logging
+  - @push.rocks/smartpath - Path utilities
+  - @push.rocks/smartpromise - Promise utilities
+  - @push.rocks/smartrx - Reactive programming
+  - @push.rocks/taskbuffer - Task management
+  - @tsclass/tsclass - TypeScript utilities
+
+## Main Components
+1. **Npmextra** - Main class for managing npmextra.json configurations
+2. **KeyValueStore** - Persistent key-value storage system
+3. **AppData** - Advanced data management with environment variable mapping
+
+## Project Structure
+- `ts/` - TypeScript source files
+- `test/` - Test files using @git.zone/tstest
+- `dist_ts/` - Compiled JavaScript output
+- `npmextra.json` - Project configuration
+- `package.json` - Node.js package configuration

.serena/memories/suggested_commands.md

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+# Suggested Commands for npmextra Development
+
+## Build Commands
+- `pnpm run build` - Build the TypeScript project (uses tsbuild)
+- `pnpm test` - Run tests using tstest
+
+## Development Commands
+- `pnpm install` - Install dependencies
+- `pnpm install --save-dev <package>` - Add development dependencies  
+- `tsx <script>` - Run TypeScript files directly (tsx is globally available)
+
+## Git Commands
+- `git status` - Check current changes
+- `git add .` - Stage changes
+- `git commit -m "message"` - Commit changes (only when explicitly requested)
+- `git mv` - Move/rename files to preserve history
+
+## Testing
+- `pnpm test` - Run all tests
+- `tstest test/test.some.ts --verbose` - Run specific test file
+- Tests use @git.zone/tstest framework with tap-based structure
+
+## Type Checking
+- `pnpm run build` - Type check and build the project
+- `tsbuild check test/**/* --skiplibcheck` - Type check test files only
+
+## Directory Structure
+- Source code in `ts/` directory
+- Tests in `test/` directory  
+- Built output in `dist_ts/` directory
+- Temporary/debug files in `.nogit/` directory

.serena/project.yml

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+# language of the project (csharp, python, rust, java, typescript, go, cpp, or ruby)
+#  * For C, use cpp
+#  * For JavaScript, use typescript
+# Special requirements:
+#  * csharp: Requires the presence of a .sln file in the project folder.
+language: typescript
+
+# whether to use the project's gitignore file to ignore files
+# Added on 2025-04-07
+ignore_all_files_in_gitignore: true
+# list of additional paths to ignore
+# same syntax as gitignore, so you can use * and **
+# Was previously called `ignored_dirs`, please update your config if you are using that.
+# Added (renamed) on 2025-04-07
+ignored_paths: []
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+
+# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions, 
+# execute `uv run scripts/print_tool_overview.py`.
+#
+#  * `activate_project`: Activates a project by name.
+#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
+#  * `create_text_file`: Creates/overwrites a file in the project directory.
+#  * `delete_lines`: Deletes a range of lines within a file.
+#  * `delete_memory`: Deletes a memory from Serena's project-specific memory store.
+#  * `execute_shell_command`: Executes a shell command.
+#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
+#  * `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
+#  * `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filtered by type).
+#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
+#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+#  * `initial_instructions`: Gets the initial instructions for the current project.
+#     Should only be used in settings where the system prompt cannot be set,
+#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+#  * `insert_at_line`: Inserts content at a given line in a file.
+#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+#  * `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
+#  * `read_file`: Reads a file within the project directory.
+#  * `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
+#  * `remove_project`: Removes a project from the Serena configuration.
+#  * `replace_lines`: Replaces a range of lines within a file with new content.
+#  * `replace_symbol_body`: Replaces the full definition of a symbol.
+#  * `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
+#  * `search_for_pattern`: Performs a search for a pattern in the project.
+#  * `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
+#  * `switch_modes`: Activates modes by providing a list of their names
+#  * `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
+#  * `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
+#  * `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
+#  * `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.
+excluded_tools: []
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ""
+
+project_name: "npmextra"