From 12a395bd414c25b1d76546a2072fe56683c5182e Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Mon, 4 Aug 2025 22:01:45 -0700 Subject: [PATCH 1/8] fix: drastically improve Mermaid diagram text contrast with dark backgrounds MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Changed to solid dark background colors with white text - VS Code Extension: Deep blue (#1976d2) with white text - MCP Server: Dark green (#388e3c) with white text - Neo4j Database: Dark orange (#f57c00) with white text - Graph Layers: Dark purple (#7b1fa2) with white text - Processing Components: Dark pink (#c2185b) with white text - Added darker stroke colors for better definition - Ensures excellent readability and accessibility Fixes #75 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 9c1f4330..30bd85cb 100644 --- a/README.md +++ b/README.md @@ -57,15 +57,15 @@ graph TB LLM --> Neo4j end - style VSCode fill:#e1f5fe - style MCP fill:#e8f5e9 - style Neo4j fill:#fff3e0 - style FS fill:#f3e5f5 - style CH fill:#f3e5f5 - style DOC fill:#f3e5f5 - style LSP fill:#fce4ec - style TS fill:#fce4ec - style LLM fill:#fce4ec + style VSCode fill:#1976d2,color:#ffffff,stroke:#0d47a1,stroke-width:2px + style MCP fill:#388e3c,color:#ffffff,stroke:#1b5e20,stroke-width:2px + style Neo4j fill:#f57c00,color:#ffffff,stroke:#e65100,stroke-width:2px + style FS fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px + style CH fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px + style DOC fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px + style LSP fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px + style TS fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px + style LLM fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px ``` ## 🔧 Components From aa51f41376766291d93919de8aa4d06c4223e2d3 Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Mon, 4 Aug 2025 22:06:19 -0700 Subject: [PATCH 2/8] fix: prevent Mermaid diagram truncation with horizontal layout MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Changed from top-bottom (TB) to left-right (LR) flowchart layout - Simplified node labels to prevent overflow - Reduced text in each box to essential information - Maintains dark backgrounds with white text for contrast - Ensures all components and connections are fully visible 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- README.md | 62 +++++++++++++++++++++++++++---------------------------- 1 file changed, 30 insertions(+), 32 deletions(-) diff --git a/README.md b/README.md index 30bd85cb..e5123a5c 100644 --- a/README.md +++ b/README.md @@ -20,43 +20,41 @@ Cue is a sophisticated code analysis tool that creates comprehensive graph repre Cue creates a sophisticated multilayer graph representation of your codebase: ```mermaid -graph TB - subgraph "Cue Architecture" - subgraph "User Interfaces" - VSCode["VS Code Extension
• 3D Visualizer
• Search/Filter
• Interactive Exploration"] - MCP["MCP Server
(AI Agents)
• Context Tools
• Query Builder
• Plan Builder
• LLM Processor"] - Neo4j["Neo4j Graph Database
• Node Storage
• Relationships
• Graph Queries
• Cypher API"] +flowchart LR + subgraph UI["User Interfaces"] + VSCode["VS Code Extension
• 3D Visualizer
• Search/Filter
• Interactive"] + MCP["MCP Server
(AI Agents)
• Context Tools
• Query Builder"] + Neo4j["Neo4j Database
• Node Storage
• Graph Queries"] + end + + subgraph Core["Cue Core Engine"] + subgraph GL["Graph Layers"] + FS["Filesystem
Layer"] + CH["Code Hierarchy
Layer"] + DOC["Documentation
Layer"] end - subgraph "Cue Core Engine" - subgraph "Graph Layers" - FS["Filesystem Layer
• Files
• Folders
• Structure"] - CH["Code Hierarchy Layer
• Classes
• Functions
• Variables"] - DOC["Documentation Layer
• Concepts
• Entities
• Auto-Link"] - end - - subgraph "Processing Components" - LSP["LSP Integration
• References
• Symbols
• Workspace"] - TS["Tree-Sitter Parsing
• AST Parse
• Language Specific"] - LLM["LLM Integration
• Summaries
• Context
• Planning"] - end + subgraph PC["Processing Components"] + LSP["LSP
Integration"] + TS["Tree-Sitter
Parsing"] + LLM["LLM
Integration"] end - - VSCode --> Core[Cue Core Engine] - MCP --> Core - Neo4j --> Core - - FS --> LSP - FS --> TS - CH --> LSP - CH --> TS - DOC --> LLM - - LSP --> Neo4j - TS --> Neo4j - LLM --> Neo4j end + VSCode --> Core + MCP --> Core + Neo4j --> Core + + FS --> LSP + FS --> TS + CH --> LSP + CH --> TS + DOC --> LLM + + LSP --> Neo4j + TS --> Neo4j + LLM --> Neo4j + style VSCode fill:#1976d2,color:#ffffff,stroke:#0d47a1,stroke-width:2px style MCP fill:#388e3c,color:#ffffff,stroke:#1b5e20,stroke-width:2px style Neo4j fill:#f57c00,color:#ffffff,stroke:#e65100,stroke-width:2px From 3dab8ce9d12fb4636c6cb3c1cf346b036524a2a4 Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Mon, 4 Aug 2025 22:08:31 -0700 Subject: [PATCH 3/8] =?UTF-8?q?fix:=20add=20missing=20Semantic=20Layer=20a?= =?UTF-8?q?nd=20AST=E2=86=92Symbols=20binding=20to=20diagram?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Added Semantic Layer with LLM Summaries and Code Descriptions - Updated Code Hierarchy Layer to show AST→Symbols binding - Connected Semantic Layer to LLM Integration component - Maintains horizontal layout and dark color scheme 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e5123a5c..55bb46b1 100644 --- a/README.md +++ b/README.md @@ -30,8 +30,9 @@ flowchart LR subgraph Core["Cue Core Engine"] subgraph GL["Graph Layers"] FS["Filesystem
Layer"] - CH["Code Hierarchy
Layer"] + CH["Code Hierarchy
• AST→Symbols
• Classes/Functions"] DOC["Documentation
Layer"] + SEM["Semantic Layer
• LLM Summaries
• Code Descriptions"] end subgraph PC["Processing Components"] @@ -50,6 +51,7 @@ flowchart LR CH --> LSP CH --> TS DOC --> LLM + SEM --> LLM LSP --> Neo4j TS --> Neo4j @@ -61,6 +63,7 @@ flowchart LR style FS fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px style CH fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px style DOC fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px + style SEM fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px style LSP fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px style TS fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px style LLM fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px From ffe28e2773a9f46919461b57e72b29ad5e9ab3b9 Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Mon, 4 Aug 2025 22:19:46 -0700 Subject: [PATCH 4/8] fix: restore vertical layout with extensibility indicator MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Restored preferred top-bottom (TB) layout - Added font size directive to help with rendering - Added "Graph Layers (Extensible)" label - Added custom layers placeholder with dashed styling - Shows example custom layers: Tests, Security, Metrics - Used dotted connections for extensibility - Maintains all layer details including AST→Symbols and Semantic Layer 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- README.md | 72 ++++++++++++++++++++++++++++++------------------------- 1 file changed, 40 insertions(+), 32 deletions(-) diff --git a/README.md b/README.md index 55bb46b1..a8d3cb4e 100644 --- a/README.md +++ b/README.md @@ -20,43 +20,50 @@ Cue is a sophisticated code analysis tool that creates comprehensive graph repre Cue creates a sophisticated multilayer graph representation of your codebase: ```mermaid -flowchart LR - subgraph UI["User Interfaces"] - VSCode["VS Code Extension
• 3D Visualizer
• Search/Filter
• Interactive"] - MCP["MCP Server
(AI Agents)
• Context Tools
• Query Builder"] - Neo4j["Neo4j Database
• Node Storage
• Graph Queries"] - end - - subgraph Core["Cue Core Engine"] - subgraph GL["Graph Layers"] - FS["Filesystem
Layer"] - CH["Code Hierarchy
• AST→Symbols
• Classes/Functions"] - DOC["Documentation
Layer"] - SEM["Semantic Layer
• LLM Summaries
• Code Descriptions"] +%%{init: {'theme':'base', 'themeVariables': { 'fontSize': '16px'}}}%% +graph TB + subgraph "Cue Architecture" + subgraph "User Interfaces" + VSCode["VS Code Extension
• 3D Visualizer
• Search/Filter
• Interactive Exploration"] + MCP["MCP Server
(AI Agents)
• Context Tools
• Query Builder
• Plan Builder
• LLM Processor"] + Neo4j["Neo4j Graph Database
• Node Storage
• Relationships
• Graph Queries
• Cypher API"] end - subgraph PC["Processing Components"] - LSP["LSP
Integration"] - TS["Tree-Sitter
Parsing"] - LLM["LLM
Integration"] + subgraph "Cue Core Engine" + subgraph "Graph Layers (Extensible)" + FS["Filesystem Layer
• Files
• Folders
• Structure"] + CH["Code Hierarchy Layer
• AST→Symbols
• Classes
• Functions
• Variables"] + DOC["Documentation Layer
• Concepts
• Entities
• Auto-Link"] + SEM["Semantic Layer
• LLM Summaries
• Code Descriptions
• Context"] + EXT["+ Add Custom Layers
• Tests Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] + end + + subgraph "Processing Components" + LSP["LSP Integration
• References
• Symbols
• Workspace"] + TS["Tree-Sitter Parsing
• AST Parse
• Language Specific"] + LLM["LLM Integration
• Summaries
• Context
• Planning"] + end end + + VSCode --> Core[Cue Core Engine] + MCP --> Core + Neo4j --> Core + + FS --> LSP + FS --> TS + CH --> LSP + CH --> TS + DOC --> LLM + SEM --> LLM + EXT -.-> LSP + EXT -.-> TS + EXT -.-> LLM + + LSP --> Neo4j + TS --> Neo4j + LLM --> Neo4j end - VSCode --> Core - MCP --> Core - Neo4j --> Core - - FS --> LSP - FS --> TS - CH --> LSP - CH --> TS - DOC --> LLM - SEM --> LLM - - LSP --> Neo4j - TS --> Neo4j - LLM --> Neo4j - style VSCode fill:#1976d2,color:#ffffff,stroke:#0d47a1,stroke-width:2px style MCP fill:#388e3c,color:#ffffff,stroke:#1b5e20,stroke-width:2px style Neo4j fill:#f57c00,color:#ffffff,stroke:#e65100,stroke-width:2px @@ -64,6 +71,7 @@ flowchart LR style CH fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px style DOC fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px style SEM fill:#7b1fa2,color:#ffffff,stroke:#4a148c,stroke-width:2px + style EXT fill:#546e7a,color:#ffffff,stroke:#37474f,stroke-width:2px,stroke-dasharray: 5 5 style LSP fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px style TS fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px style LLM fill:#c2185b,color:#ffffff,stroke:#880e4f,stroke-width:2px From ab6145d29ba0c084f60b6f7f0b42e63da40b7e38 Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Mon, 4 Aug 2025 22:25:40 -0700 Subject: [PATCH 5/8] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a8d3cb4e..1bec6371 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ graph TB CH["Code Hierarchy Layer
• AST→Symbols
• Classes
• Functions
• Variables"] DOC["Documentation Layer
• Concepts
• Entities
• Auto-Link"] SEM["Semantic Layer
• LLM Summaries
• Code Descriptions
• Context"] - EXT["+ Add Custom Layers
• Tests Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] + EXT["\+ Add Custom Layers
• Github PR Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] end subgraph "Processing Components" From 8708ce28f00e92aa3e08e9feb44831c04a07e74a Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Tue, 5 Aug 2025 06:33:58 -0700 Subject: [PATCH 6/8] fix: add direct Neo4j connections and move extensions to bottom MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Added direct connections from VS Code Extension to Neo4j - Added direct connections from MCP Server to Neo4j - Moved custom layers extension box to the bottom of Core Engine - Shows that both user interfaces can query Neo4j directly - Maintains all other improvements and connections 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1bec6371..5eb1ed6a 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,6 @@ graph TB CH["Code Hierarchy Layer
• AST→Symbols
• Classes
• Functions
• Variables"] DOC["Documentation Layer
• Concepts
• Entities
• Auto-Link"] SEM["Semantic Layer
• LLM Summaries
• Code Descriptions
• Context"] - EXT["\+ Add Custom Layers
• Github PR Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] end subgraph "Processing Components" @@ -43,10 +42,14 @@ graph TB TS["Tree-Sitter Parsing
• AST Parse
• Language Specific"] LLM["LLM Integration
• Summaries
• Context
• Planning"] end + + EXT["+ Add Custom Layers
• Github PR Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] end VSCode --> Core[Cue Core Engine] + VSCode --> Neo4j MCP --> Core + MCP --> Neo4j Neo4j --> Core FS --> LSP From 88c45445c1f3c5591dc2675e64c35d40e20a39e2 Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Tue, 5 Aug 2025 09:01:39 -0700 Subject: [PATCH 7/8] chore: add VS Code test directories to gitignore MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Added .vscode-test/ for root level VS Code test directories - Added vscode-*/.vscode-test/ to ignore test directories in VS Code extension folders - Prevents VS Code test artifacts from being tracked in git 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index b7ebb541..8991d7ce 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,8 @@ lsp-ws-proxy/ ruby-on-rails-sample-app/ .python-version .vscode/ +.vscode-test/ +vscode-*/.vscode-test/ .idea/ dist/ fil-result/ From 25ebef9465138359ab368f36df93811c20e1e26b Mon Sep 17 00:00:00 2001 From: Ryan Sweet Date: Tue, 5 Aug 2025 09:23:52 -0700 Subject: [PATCH 8/8] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5eb1ed6a..e1936672 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Cue +# CUE - the Code-Understanding-Engine > Transform any codebase into an intelligent multilayer graph for AI-powered code understanding @@ -43,7 +43,7 @@ graph TB LLM["LLM Integration
• Summaries
• Context
• Planning"] end - EXT["+ Add Custom Layers
• Github PR Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] + EXT["\+ Add Custom Layers
• Github PR Layer
• Security Layer
• Metrics Layer
• Your Layer Here"] end VSCode --> Core[Cue Core Engine]