Enhance file organizer workflow and refactor node architecture for v0.8.0 (#34)

* Add comprehensive environment management system with default and graph-specific environments

* Fix virtual environment path resolution for development and compiled modes

* Fix environment selection dialog timing - defer until after GUI loads

* Update main application for environment system compatibility

* Improve toolbar layout and radio button styling

- Move execution controls to right side of toolbar with spacer
- Fix radio buttons to always use circular indicators
- Improve text contrast and readability for execution mode selection
- Add proper hover states and consistent sizing for radio buttons

* Optimize live mode performance and reduce button click delays

- Add UI update throttling to prevent redundant live mode updates
- Cache environment validation results to avoid repeated file system checks
- Optimize event handler setup to be incremental, not full rebuild
- Reduce logging spam during live mode activation
- Keep event handlers persistent for faster mode switching
- Fix performance regression introduced by environment management system

* Improve execution button visibility and remove emoji icons

- Change button text color to black for better visibility on bright backgrounds
- Remove emoji icons from all execution button text states
- Keep white text only on red (paused) button for contrast
- Update all button states: Execute Graph, Start Live Mode, Pause/Resume, etc.

* Rename Run menu to Environment menu for better clarity

- Changed 'Run' menu to 'Environment' menu since it only contains environment management
- More descriptive and intuitive menu organization
- Better reflects the actual functionality contained within

* Implement comprehensive graph description editing and fix paragraph spacing

- Add graph description extraction from markdown H1 titles and following paragraphs
- Implement Graph Properties dialog accessible via File → Graph Properties menu
- Fix paragraph spacing preservation in both node and graph descriptions
- Update FlowFormatHandler to properly parse and generate graph metadata
- Ensure copy/paste operations exclude graph descriptions as requested
- Add proper paragraph break handling with double newlines between paragraphs
- Rename json_to_flow/flow_to_json methods to data_to_markdown/markdown_to_data
- Include actual node descriptions in saved markdown instead of placeholder text

🤖 Generated with [Claude Code](https://claude.ai/code)

* Add node description editing capability

- Add description field to Node class with serialization support
- Enhance Node Properties dialog with description editor (QTextEdit)
- Update dialog constructor to accept and display node descriptions
- Preserve node descriptions in save/load cycle
- Support markdown formatting in node description editor

🤖 Generated with [Claude Code](https://claude.ai/code)

* Remove JSON file format support and update file operations

- Remove JSON file format from save/load dialogs (only .md files supported)
- Update _save_file() to use actual graph title/description instead of defaults
- Simplify _load_file() to only handle .md format using FlowFormatHandler
- Use data_to_markdown() and markdown_to_data() method names consistently
- Ensure graph metadata is properly preserved during save/load operations

🤖 Generated with [Claude Code](https://claude.ai/code)

* Improve view state persistence and add comprehensive testing

- Update save_view_state() to accept optional file_path parameter
- Simplify view state loading logic with robust transform and center point handling
- Add comprehensive GUI-based test for view state persistence functionality
- Test covers zoom/pan operations, file switching, and state restoration
- Ensure view state is properly saved when switching between files

🤖 Generated with [Claude Code](https://claude.ai/code)

* Update password generator example with comprehensive descriptions

- Add detailed graph description explaining the complete workflow
- Enhance node descriptions with multi-paragraph technical details
- Include implementation specifics for each component
- Demonstrate proper paragraph spacing in descriptions
- Update node positions and GUI state after testing

🤖 Generated with [Claude Code](https://claude.ai/code)

* Fix virtual environment dialog and view state persistence issues

- Fixed startup venv dialog not showing for new/example graphs
- Added proper environment selection prompts before execution
- Fixed QSettings path errors in environment manager using correct project root detection
- Fixed view state (pan/zoom) not being restored when loading last saved graph on startup
- Set default environment to True for new/untitled graphs
- Added ensure_environment_selected() method called before execution

* Fix pin generation for complex generic types and improve example graphs

Two major fixes for the pin generation system:

1. Fix _parse_type_hint() method to properly handle complex generic types like List[Dict]:
   - Added support for ast.Name slices (simple generics)
   - Added support for ast.Tuple slices (multiple parameters)
   - Added fallback handling for other slice structures

2. Fix update_pins_from_code() logic error for List/Tuple detection:
   - Changed to only treat Tuple types as multiple outputs
   - Handle List[Dict] and other single-element generics correctly
   - Prevents AttributeError when accessing .elts on non-Tuple slices

Example graph improvements:
- Fixed missing GUI State Handler functions (set_values, set_initial_state)
- Connected data-generator to rest of analysis pipeline
- Removed non-functional buttons from dashboard and password generator
- Updated node positions and metadata from GUI testing

🤖 Generated with [Claude Code](https://claude.ai/code)

* Fix file organizer automation workflow and refactor node architecture

- Add missing workflow starter entry point node for clean initiation
- Fix broken data flow connections between all nodes in pipeline
- Refactor complex @node_entry functions following FlowSpec best practices:
  * File Categorizer: Extract FileCategorizer class with modular methods
  * File Mover: Extract FileOrganizer class with specialized operations
  * Operation Verifier: Extract OrganizationVerifier class with focused methods
- Add comprehensive error handling and validation throughout workflow
- Enhance GUI elements with tooltips and better user experience
- Fix folder scanner to return tuple with both file list and base path
- Add operation verification node for post-organization validation
- Create complete data pipeline: Scanner → Categorizer → Creator → Mover → Verifier
- Ensure all pin connections properly match function signatures
- Improve code maintainability and testability with helper classes

🤖 Generated with [Claude Code](https://claude.ai/code)

---------

Co-authored-by: Bryan Howard <[email protected]>

Author: bhowiebkr

examples/data_analysis_dashboard.md

@@ -19,20 +19,20 @@ The node serves as a data source for testing downstream analytics components wit
   "uuid": "data-generator",
   "title": "Sample Data Generator",
   "pos": [
-    100.0,
-    200.0
+    -46.05000000000001,
+    220.70000000000005
   ],
   "size": [
     250,
-    190
+    265
   ],
   "colors": {
     "title": "#007bff",
     "body": "#0056b3"
   },
   "gui_state": {
     "num_records": 100,
-    "data_type": "Sales"
+    "data_type": "Weather"
   }
 }
 ```
@@ -111,6 +111,10 @@ def get_values(widgets):
         'data_type': widgets['data_type'].currentText()
     }
 
+def set_values(widgets, outputs):
+    # Data generator doesn't need to display outputs
+    pass
+
 def set_initial_state(widgets, state):
     widgets['num_records'].setValue(state.get('num_records', 100))
     widgets['data_type'].setCurrentText(state.get('data_type', 'Sales'))
@@ -132,8 +136,8 @@ Returns three outputs: statistics dictionary with calculated metrics, total reco
   "uuid": "statistics-calculator",
   "title": "Statistics Calculator",
   "pos": [
-    450.0,
-    100.0
+    295.9000000000001,
+    123.0
   ],
   "size": [
     250,
@@ -212,8 +216,8 @@ Returns three outputs: trends dictionary containing monthly distributions, patte
   "uuid": "trend-analyzer",
   "title": "Trend Analyzer",
   "pos": [
-    450.0,
-    400.0
+    643.1999999999998,
+    324.1000000000001
   ],
   "size": [
     250,
@@ -302,12 +306,12 @@ Outputs a single formatted string suitable for display in QTextEdit widgets. The
   "uuid": "dashboard-display",
   "title": "Analytics Dashboard",
   "pos": [
-    850.0,
-    250.0
+    1017.9,
+    143.04999999999998
   ],
   "size": [
-    276,
-    589
+    270.1,
+    581.45
   ],
   "colors": {
     "title": "#6c757d",
@@ -394,12 +398,6 @@ widgets['dashboard_display'].setPlainText('Generate data and run analysis to see
 font = QFont('Courier New', 9)
 widgets['dashboard_display'].setFont(font)
 layout.addWidget(widgets['dashboard_display'])
-
-widgets['export_btn'] = QPushButton('Export Report', parent)
-layout.addWidget(widgets['export_btn'])
-
-widgets['refresh_btn'] = QPushButton('Refresh Analysis', parent)
-layout.addWidget(widgets['refresh_btn'])
 ```
 
 ### GUI State Handler
@@ -411,16 +409,44 @@ def get_values(widgets):
 def set_values(widgets, outputs):
     dashboard = outputs.get('output_1', 'No dashboard data')
     widgets['dashboard_display'].setPlainText(dashboard)
+
+def set_initial_state(widgets, state):
+    # Dashboard doesn't have saved state to restore
+    pass
 ```
 
 
 ## Connections
 
 ```json
 [
+  {
+    "start_node_uuid": "data-generator",
+    "start_pin_name": "exec_out",
+    "end_node_uuid": "statistics-calculator",
+    "end_pin_name": "exec_in"
+  },
+  {
+    "start_node_uuid": "data-generator",
+    "start_pin_name": "output_1",
+    "end_node_uuid": "statistics-calculator",
+    "end_pin_name": "data"
+  },
   {
     "start_node_uuid": "statistics-calculator",
     "start_pin_name": "exec_out",
+    "end_node_uuid": "trend-analyzer",
+    "end_pin_name": "exec_in"
+  },
+  {
+    "start_node_uuid": "data-generator",
+    "start_pin_name": "output_1",
+    "end_node_uuid": "trend-analyzer",
+    "end_pin_name": "data"
+  },
+  {
+    "start_node_uuid": "trend-analyzer",
+    "start_pin_name": "exec_out",
     "end_node_uuid": "dashboard-display",
     "end_pin_name": "exec_in"
   },