diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 087f0615..180b752f 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -31,8 +31,7 @@
       }
     }
   },
-  "initializeCommand": "git submodule update --init --recursive",
-  "postCreateCommand": "rustc --version && cargo --version && git submodule update --init --recursive && cd editors/vscode-lsp && npm install && cd ../.. && ([ -d packages/diagram-core ] && cd packages/diagram-core && bun install || true) && ([ -d packages/diagram-ui ] && cd packages/diagram-ui && bun install || true)",
+  "initializeCommand": "git submodule deinit -f --all 2>/dev/null || true && git submodule update --init --recursive",
   "forwardPorts": [3000, 5173],
   "remoteUser": "vscode"
-}
+}
\ No newline at end of file
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 0004a5f9..2a42c56f 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -18,18 +18,21 @@ Syster is a comprehensive Rust-based parser and tooling suite for SysML v2 (Syst
 - **LSP:** async-lsp library for Language Server Protocol
 - **Formatter:** Rowan-based Concrete Syntax Tree (CST)
 - **VS Code Extension:** TypeScript, Node.js
-- **Build System:** Cargo workspace with 3 crates
+- **Build System:** Independent submodules, each with own Cargo.toml/package.json
 
 ## Repository Structure
 
 ```
 syster/
-├── crates/
-│   ├── syster-base/      # Core library (parser, AST, semantic analysis)
-│   ├── syster-cli/       # Command-line tool
-│   └── syster-lsp/       # Language Server Protocol implementation
-├── editors/vscode/       # VS Code extension
-├── docs/                 # Documentation
+├── base/                 # syster-base: parser, AST, semantic analysis
+├── cli/                  # syster-cli: command-line tool
+├── language-server/      # syster-lsp: Language Server Protocol implementation
+├── language-client/      # VS Code LSP extension
+├── modeller/             # VS Code modeller extension
+├── viewer/               # VS Code viewer extension
+├── diagram-core/         # TypeScript diagram utilities
+├── diagram-ui/           # React diagram components
+├── pipelines/            # CI/CD pipeline definitions
 └── .github/              # GitHub configuration and instructions
 ```
 
@@ -165,7 +168,7 @@ Before making changes, review:
 
 ## VS Code Extension
 
-Located in `editors/vscode/`:
+Located in `language-client/`:
 - TypeScript-based extension
 - Integrates with syster-lsp server
 - Provides syntax highlighting, IntelliSense, formatting, and more
@@ -173,7 +176,7 @@ Located in `editors/vscode/`:
 
 ## Standard Library
 
-The `crates/syster-base/sysml.library/` directory contains the SysML v2 standard library files. These are loaded automatically by the workspace when needed.
+The `base/sysml.library/` directory contains the SysML v2 standard library files. These are loaded automatically by the workspace when needed.
 
 ## Getting Help
 
diff --git a/.github/instructions/chore.md b/.github/instructions/chore.md
deleted file mode 100644
index dbd977a7..00000000
--- a/.github/instructions/chore.md
+++ /dev/null
@@ -1,61 +0,0 @@
----
-applyTo: '**/*.rs'
----
-
-# Pre-Commit Checklist
-
-This checklist MUST be completed after every task/todo before committing changes.
-
-## Code Quality Checks
-
-- [ ] Remove unnecessary documentation from each changed file
-  - Delete redundant comments that don't add value
-  - Keep only essential API docs and complex logic explanations
-  
-- [ ] Remove unused methods (unless marked with TODO prefix)
-  - Search for `#[allow(dead_code)]` warnings
-  - Delete or mark for future use with `// TODO: ...`
-  
-- [ ] Move tests into their own test files
-  - Inline tests → `<module>/tests.rs`
-  - Keep test modules focused and organized
-
-## Test Quality Checks
-
-- [ ] Add missing tests for each changed file
-  - Every public function should have at least one test
-  - Cover edge cases and error paths
-  
-- [ ] Remove if-else match logic from tests
-  - Use `let-else` pattern: `let Some(x) = y else { panic!("...") };`
-  - Use `assert_matches!` macro where appropriate
-  
-- [ ] Make tests more concrete
-  - Replace `assert!(x >= 5)` with `assert_eq!(x, 5)`
-  - Use exact values instead of ranges when possible
-  - Make assertions specific and meaningful
-
-## Final Checks
-
-- [ ] Address any TODOs added during the task
-  - Either implement them or file as future work
-  - Document why TODOs remain if not addressed
-  
-- [ ] Clean up any temporary notes or debug code
-  - Remove `println!` debug statements
-  - Remove commented-out code blocks
-  - Clean up experimental code
-
-## Repeat Process
-
-Iterate through this checklist until no further changes are needed.
-
-## Validation
-
-After completing checklist:
-```bash
-cargo clippy --fix --allow-dirty
-cargo test
-git add -A && git commit -m "..."
-```
-
diff --git a/.github/instructions/configuration.md b/.github/instructions/configuration.md
deleted file mode 100644
index d08794c4..00000000
--- a/.github/instructions/configuration.md
+++ /dev/null
@@ -1,378 +0,0 @@
----
-applyTo: '**/{Cargo.toml,package.json,tsconfig.json,.gitignore,Makefile}'
----
-
-# Configuration Files Guidelines
-
-## Overview
-
-This file provides guidance for working with configuration files in the Syster repository. These files define build settings, dependencies, linting rules, and project structure.
-
-## Cargo.toml Files
-
-### Workspace Root (Cargo.toml)
-
-The root `Cargo.toml` defines:
-- Workspace members (all crates)
-- Shared workspace package metadata
-- Workspace-wide linter rules (clippy)
-- Build optimization profiles
-
-**Key Principles:**
-- Keep workspace metadata centralized
-- Use consistent versioning across crates
-- Define strict clippy rules for code quality
-- Optimize profiles for development vs. production
-
-### Workspace Lints
-
-Current clippy rules enforce:
-```toml
-# Enforce explicit error handling
-unwrap_used = "warn"           # Avoid .unwrap() in production code
-expect_used = "warn"           # Avoid .expect() in production code  
-panic = "warn"                 # Avoid panic!() in production code
-todo = "warn"                  # Mark incomplete code
-unimplemented = "warn"         # Mark unimplemented code
-
-# Code quality
-dbg_macro = "warn"             # Remove debug macros
-print_stdout = "warn"          # Avoid print to stdout
-print_stderr = "warn"          # Avoid print to stderr
-missing_errors_doc = "warn"    # Document error conditions
-missing_panics_doc = "warn"    # Document panic conditions
-
-# Performance
-inefficient_to_string = "warn"
-unnecessary_wraps = "warn"
-
-# Style consistency
-enum_glob_use = "warn"
-wildcard_imports = "warn"
-
-# Test quality
-collapsible_if = "warn"
-collapsible_else_if = "warn"
-cognitive_complexity = "deny"  # Keep functions simple
-
-# Deny by category (set explicit priority to avoid ambiguity)
-correctness = { level = "deny", priority = -1 }  # Critical errors
-suspicious = { level = "deny", priority = -1 }
-complexity = { level = "deny", priority = -1 }
-perf = { level = "deny", priority = -1 }
-```
-
-**When adding new lints:**
-- Justify why it improves code quality
-- Test across the entire workspace
-- Document in comments if non-obvious
-- Use `warn` for style, `deny` for correctness
-
-### Build Profiles
-
-```toml
-[profile.dev]           # Fast compilation for development
-[profile.test]          # Test optimization
-[profile.release]       # Balanced for containers
-[profile.production]    # Maximum optimization (may fail in low memory)
-```
-
-**Don't modify profiles unless:**
-- Compilation is too slow
-- Runtime performance is problematic
-- Memory constraints require changes
-
-### Per-Crate Cargo.toml
-
-Each crate (`syster-base`, `syster-cli`, `syster-lsp`) has its own `Cargo.toml`:
-
-```toml
-[package]
-name = "syster-base"
-version.workspace = true        # Use workspace version
-edition.workspace = true        # Use workspace edition
-
-[dependencies]
-# Core dependencies
-pest = "2.7"                   # Parser generator
-# ... other deps
-
-[dev-dependencies]
-# Test-only dependencies
-rstest = "0.18"               # Test fixtures
-```
-
-**Guidelines:**
-- Use `workspace = true` for version, edition, authors, license
-- Group dependencies logically (parser, semantic, LSP, etc.)
-- Specify minimum required version
-- Keep dev-dependencies separate
-- Document non-obvious dependency choices
-
-## package.json (VS Code Extension)
-
-Located in `editors/vscode/package.json`, this defines:
-- Extension metadata (name, version, description)
-- VS Code engine compatibility
-- Extension activation events
-- Language definitions
-- Configuration settings
-- Commands and contributions
-
-**Key Sections:**
-
-### Extension Metadata
-```json
-{
-  "name": "sysml-language-support",
-  "displayName": "SysML v2 Language Support",
-  "version": "0.1.0",
-  "engines": {
-    "vscode": "^1.85.0"  // Minimum VS Code version
-  }
-}
-```
-
-### Language Contributions
-```json
-{
-  "contributes": {
-    "languages": [{
-      "id": "sysml",
-      "extensions": [".sysml"],
-      "aliases": ["SysML", "sysml"]
-    }]
-  }
-}
-```
-
-### Configuration Settings
-```json
-{
-  "contributes": {
-    "configuration": {
-      "properties": {
-        "syster.stdlib.enabled": {
-          "type": "boolean",
-          "default": true,
-          "description": "Load SysML standard library on document open"
-        },
-        "syster.stdlib.path": {
-          "type": "string",
-          "default": "",
-          "description": "Custom path to SysML standard library directory"
-        },
-        "syster.lsp.path": {
-          "type": "string",
-          "default": "/workspaces/syster/target/release/syster-lsp",
-          "description": "Path to syster-lsp binary"
-        }
-      }
-    }
-  }
-}
-```
-
-**When modifying package.json:**
-- Validate JSON syntax
-- Test activation events carefully (affects startup time)
-- Keep settings prefixed with `sysml.`
-- Provide clear descriptions for user-facing settings
-- Update README.md if adding new features
-
-## tsconfig.json (TypeScript Configuration)
-
-Controls TypeScript compilation for the VS Code extension:
-
-```json
-{
-  "compilerOptions": {
-    "module": "commonjs",
-    "target": "ES2020",
-    "strict": true,
-    "outDir": "out"
-  }
-}
-```
-
-**Guidelines:**
-- Keep `strict: true` for type safety
-- Don't lower target below ES2020
-- Use `outDir` for compiled output
-- Enable source maps for debugging
-
-## Makefile
-
-Provides convenient commands for common tasks:
-
-```makefile
-build:           # Build the project
-test:            # Run tests
-fmt:             # Format code
-lint:            # Run clippy
-run-guidelines:  # Full validation pipeline
-```
-
-**Guidelines:**
-- Keep targets simple and focused
-- Use `.PHONY` for non-file targets
-- Add helpful comments for each target
-- Show progress for multi-step targets
-- Don't duplicate functionality that's better in Cargo
-
-**When adding new targets:**
-1. Choose a clear, descriptive name
-2. Add to help text
-3. Test that it works
-4. Document any dependencies
-
-## .gitignore
-
-Controls which files Git tracks:
-
-**Current patterns:**
-- `/target/` - Rust build artifacts
-- `*.swp`, `*.swo` - Editor temporary files
-- `Cargo.lock` in libraries (keep in binaries)
-- `node_modules/` - npm dependencies
-- `.DS_Store` - macOS files
-
-**When modifying:**
-- Add patterns for new build tools
-- Don't ignore files that should be committed
-- Use comments to explain non-obvious patterns
-- Test with `git status` to verify
-
-**Common additions:**
-```gitignore
-# IDE files
-.vscode/settings.json  # But keep .vscode/extensions.json
-.idea/
-
-# Build artifacts  
-/out/
-/dist/
-*.vsix
-
-# OS files
-Thumbs.db
-```
-
-## Configuration Best Practices
-
-### Version Management
-- Use workspace versioning for consistent releases
-- Keep versions in sync across related crates
-- Bump versions following semantic versioning:
-  - MAJOR: Breaking changes
-  - MINOR: New features, backward compatible
-  - PATCH: Bug fixes
-
-### Dependency Management
-- Specify minimum required versions
-- Avoid overly restrictive version constraints
-- Keep dependencies up-to-date for security
-- Review new dependencies carefully
-- Document why non-obvious dependencies are needed
-
-### Testing Configuration Changes
-Before committing configuration changes:
-```bash
-# Test Cargo changes
-cargo check --workspace
-cargo test --workspace
-cargo clippy --workspace
-
-# Test package.json changes
-cd editors/vscode
-npm install
-npm run compile
-
-# Test Makefile changes
-make build
-make test
-make run-guidelines
-```
-
-### Common Pitfalls
-
-❌ **Don't:**
-- Change profile settings without understanding impact
-- Add dependencies without considering alternatives
-- Modify linter rules to silence warnings (fix the code instead)
-- Use wildcard version constraints (`*` or `>=x.0`)
-- Add configuration options without documentation
-
-✅ **Do:**
-- Test configuration changes thoroughly
-- Document non-obvious settings
-- Keep configurations minimal and focused
-- Use workspace features to avoid duplication
-- Follow established patterns in the codebase
-
-## File-Specific Guidelines
-
-### When to Edit Cargo.toml
-- Adding or removing dependencies
-- Updating dependency versions
-- Changing build profile settings
-- Adding new crate features
-- Modifying metadata or lints
-
-### When to Edit package.json
-- Adding new VS Code commands
-- Adding configuration settings
-- Updating extension metadata
-- Changing activation events
-- Adding language definitions
-
-### When to Edit Makefile
-- Adding convenience commands
-- Simplifying complex workflows
-- Creating shortcuts for testing
-- Adding validation pipelines
-- Improving developer experience
-
-### When to Edit .gitignore
-- New build tools generate artifacts
-- IDE creates temporary files
-- OS-specific files appear
-- New dependency managers used
-- Build output changes location
-
-## Validation
-
-After modifying configuration files:
-
-```bash
-# Validate Cargo.toml syntax
-cargo check
-
-# Validate package.json syntax
-npm install --dry-run
-
-# Validate tsconfig.json
-npx tsc --noEmit
-
-# Validate Makefile
-make --dry-run <target>
-
-# Verify .gitignore works
-git status  # Should show only tracked files
-```
-
-## Security Considerations
-
-- Never commit secrets or credentials
-- Don't expose internal paths in public configs
-- Be careful with git-ignored files (ensure secrets are ignored)
-- Review dependencies for known vulnerabilities
-- Keep dependencies up-to-date
-
-## Documentation
-
-When changing configuration files:
-- Update README.md if user-facing features change
-- Update CONTRIBUTING.md if developer workflow changes
-- Document new configuration options
-- Explain why changes were made in commit messages
diff --git a/.github/instructions/copilot-instructions.md b/.github/instructions/copilot-instructions.md
deleted file mode 100644
index 23e093f8..00000000
--- a/.github/instructions/copilot-instructions.md
+++ /dev/null
@@ -1,225 +0,0 @@
----
-applyTo: '**/*.rs'
----
-
-# Rust Development Instructions
-
-## Project-Specific Guidance
-
-### Architecture Understanding - READ FIRST
-
-Before making changes, familiarize yourself with the project architecture:
-
-- **[ARCHITECTURE.md](../../ARCHITECTURE.md)** - System design, three-phase pipeline, design decisions
-- **[docs/CONTRIBUTING.md](../../docs/CONTRIBUTING.md)** - Development workflow, code conventions
-- **[docs/SYSML_PRIMER.md](../../docs/SYSML_PRIMER.md)** - SysML v2 and KerML concepts
-
-### Key Project Patterns
-
-1. **Three-Phase Pipeline**: Parse (Pest) → Syntax (AST) → Semantic (Symbols + Graphs)
-   - **Never mix phases**: Don't add semantic logic to parser, don't parse in semantic analyzer
-   - Each phase has clear inputs and outputs (see ARCHITECTURE.md)
-
-2. **Symbol Table is Global**: AST nodes don't contain resolved references
-   - Symbols are stored in centralized `SymbolTable`
-   - Use qualified names (`QualifiedName`) for cross-file references
-   - Don't add back-references to AST nodes
-
-3. **Relationship Graphs**: Use separate graphs for relationships
-   - Don't store specialization/typing in Symbol enum
-   - Use `RelationshipGraph` methods for queries
-   - Graph operations are in `src/semantic/graph.rs`
-
-4. **Import Resolution**: Three-pass algorithm (see SEMANTIC_ANALYSIS.md)
-   - Pass 1: Namespace imports (`Package::*`)
-   - Pass 2: Member imports (`Package::Member`)
-   - Pass 3: Recursive imports (`Package::*::**`)
-   - Don't try to resolve imports in a single pass
-
-5. **Type Aliases**: Use documented type aliases for clarity
-   - `QualifiedName` for fully qualified names
-   - `SimpleName` for unqualified names
-   - `ScopeId` for scope identifiers
-   - `SourceFilePath` for file paths
-
-### Adding New Features
-
-**Adding a new SysML element type** (e.g., `concern def`):
-1. Update grammar: `src/parser/sysml.pest`
-2. Define AST struct: `src/language/sysml/syntax/types.rs`
-3. Add to parent enum: `src/language/sysml/syntax/enums.rs`
-4. Update populator: `src/language/sysml/populator.rs`
-5. Add tests: `tests/semantic/sysml_parsing_tests.rs`
-
-**Adding a new semantic check**:
-1. Add error kind: `src/semantic/error.rs`
-2. Implement check: `src/semantic/analyzer.rs`
-3. Call from `analyze()` method
-4. Add tests: `tests/semantic/mod.rs`
-
-See ARCHITECTURE.md "Common Operations Guide" for detailed examples.
-
-### Module Organization
-
-```
-src/
-├── parser/          # Pest grammar files (kerml.pest, sysml.pest)
-├── language/        # Language-specific AST and populators
-│   ├── kerml/       # KerML foundation language
-│   └── sysml/       # SysML v2 systems language
-├── semantic/        # Semantic analysis (YOU ARE HERE most of the time)
-│   ├── symbol_table.rs  # Global symbol registry
-│   ├── graph.rs         # Relationship graphs
-│   ├── resolver.rs      # Name resolution
-│   ├── analyzer.rs      # Validation passes
-│   └── workspace.rs     # Multi-file coordination
-└── project/         # Workspace loading (stdlib, user projects)
-```
-
-### Common Pitfalls
-
-❌ **Don't**: Add semantic logic to AST nodes
-✅ **Do**: Keep AST immutable, use SymbolTable for semantic info
-
-❌ **Don't**: Resolve imports while building symbol table
-✅ **Do**: Build symbol table first, then run three-pass import resolution
-
-❌ **Don't**: Store relationships in Symbol enum
-✅ **Do**: Use RelationshipGraph for all relationships
-
-❌ **Don't**: Create circular dependencies between modules
-✅ **Do**: Follow dependency flow: parser → language → semantic
-
-### Terminology (SysML/KerML Specific)
-
-- **Qualified Name**: Full path like `Package::Class::Feature`
-- **Classifier**: KerML type that can have features (class, struct, etc.)
-- **Definition**: SysML type (part def, port def, action def, etc.)
-- **Usage**: SysML instance (part, port, action, etc.)
-- **Feature**: Property or operation of a classifier
-- **Specialization**: IS-A relationship (inheritance)
-- **Typing**: INSTANCE-OF relationship
-- **Subsetting**: REFINES relationship
-- **Redefinition**: OVERRIDES relationship
-
-See SYSML_PRIMER.md for full glossary.
-
-## Test-Driven Development (TDD) - MANDATORY
-
-1. **Always write tests first** before implementing functionality
-   - Write a failing test that describes the desired behavior
-   - Run the test to confirm it fails for the right reason
-   - Implement the minimal code to make the test pass
-   - Refactor if needed while keeping tests green
-
-2. **Test execution is required**
-   - After writing a test, you MUST run it using `runTests` tool or `cargo test`
-   - Never proceed to implementation without seeing the test fail first
-   - Never claim completion without running tests to verify success
-
-## Incremental Development - STRICT LIMITS
-
-1. **One function at a time**
-   - Edit only ONE function per change cycle
-   - Complete the full TDD cycle (test → implement → verify) for that function
-   - Do not move to the next function until current one is complete and tested
-
-2. **Small, focused changes**
-   - Each change should be minimal and focused
-   - If a change requires modifying multiple functions, STOP and break it down
-   - Prefer multiple small commits over one large change
-
-3. **Restart trigger**
-   - If you find yourself making changes across multiple files simultaneously, STOP
-   - If you're modifying more than ~10-15 lines in a single function, STOP and reconsider
-   - If the scope is growing beyond the original small task, STOP and restart with a smaller goal
-   - Ask the user to break down the task into smaller pieces if needed
-
-## Rust Best Practices
-
-1. **Error handling**
-   - Use `Result<T, E>` for fallible operations
-   - Use `Option<T>` for values that may or may not exist
-   - Avoid `.unwrap()` and `.expect()` in production code (tests are okay)
-   - Propagate errors with `?` operator when appropriate
-
-2. **Ownership and borrowing**
-   - Prefer borrowing (`&T`, `&mut T`) over transferring ownership
-   - Use `.clone()` judiciously - only when necessary
-   - Leverage the borrow checker to ensure memory safety
-
-3. **Idiomatic Rust**
-   - Use iterator methods (`.map()`, `.filter()`, `.collect()`) over explicit loops when clearer
-   - Prefer pattern matching over if-let chains
-   - Use `derive` macros for common traits (Debug, Clone, PartialEq, etc.)
-   - Follow Rust naming conventions (snake_case for functions/variables, CamelCase for types)
-
-4. **Code organization**
-   - Keep modules focused and cohesive
-   - Use `mod.rs` or module files appropriately
-   - Make items private by default, expose only what's needed
-   - Document public APIs with doc comments (`///`)
-
-## Workflow Checklist
-
-Before each change:
-- [ ] Have I identified ONE specific function to modify?
-- [ ] Have I written a test for this change?
-- [ ] Is this change small enough (< 15 lines in the function)?
-
-After each change:
-- [ ] Did I run the tests?
-- [ ] Did the tests pass?
-- [ ] Is the code formatted with `cargo fmt`?
-- [ ] Does `cargo clippy` pass without warnings?
-
-If you answer "no" to any of these, STOP and address it before proceeding.
-
-## Task Completion Workflow - MANDATORY
-
-After completing EACH todo/task, you MUST:
-
-1. **Complete the pre-commit checklist** (see `.github/instructions/chore.md`):
-   - Remove unnecessary documentation from each changed file
-   - Remove unused methods that don't have a TODO prefix
-   - Move tests into their own files if that hasn't been done
-   - Go through each changed file and add any missing tests
-   - Remove if-else match logic from tests
-   - Make tests more concrete (clear equals values rather than >=/<= comparisons)
-   - Address any TODOs added during the task
-   - Clean up any temporary notes
-
-2. **Run validation**: `make run-guidelines` or `cargo clippy && cargo test`
-
-3. **Commit changes**: `git add -A && git commit` with descriptive message
-
-**This is mandatory after every todo completion.** Do not skip these steps.
-
-Example commit message format:
-```
-feat(component): brief description of what was done
-
-- Detail 1
-- Detail 2
-- Tests: X passing
-```
-
-## Development Commands
-
-- `cargo test` - Run all tests
-- `cargo test <name>` - Run specific test
-- `cargo fmt` - Format code
-- `cargo clippy` - Run linter
-- `cargo build` - Build project
-- `cargo run` - Run the application
-
-## Red Flags - When to STOP
-
-⛔ You're editing multiple functions simultaneously
-⛔ You're making changes across multiple modules at once  
-⛔ The diff is growing beyond 20-30 lines
-⛔ You haven't run tests in the last change cycle
-⛔ You're implementing before writing tests
-⛔ You're unsure how to test the change
-
-**When you see these flags, pause and restart with a smaller scope.**
diff --git a/.github/instructions/documentation.md b/.github/instructions/documentation.md
deleted file mode 100644
index 59dd9ccf..00000000
--- a/.github/instructions/documentation.md
+++ /dev/null
@@ -1,420 +0,0 @@
----
-applyTo: '**/*.md'
----
-
-# Documentation Guidelines
-
-## Documentation Philosophy
-
-Documentation in Syster should be:
-- **Clear and concise** - Get to the point quickly
-- **Up-to-date** - Keep in sync with code changes
-- **Actionable** - Provide concrete examples and commands
-- **Well-organized** - Use consistent structure and hierarchy
-
-## Key Documentation Files
-
-### Repository Root
-- **README.md** - Project overview, features, quick start, usage examples
-- **ARCHITECTURE.md** - System design, core patterns, critical rules, common operations
-- **LICENSE.md** - MIT license information
-
-### docs/ Directory
-- **CONTRIBUTING.md** - Development workflow, TDD guidelines, code conventions
-- **SYSML_PRIMER.md** - SysML v2 and KerML concepts for developers new to the domain
-- **FUTURE_WORK.md** - Planned features and improvements
-
-### .github/
-- **copilot-instructions.md** - Repository-wide Copilot guidance
-- **instructions/*.md** - Path-specific Copilot instructions
-
-### Per-Crate Documentation
-- **crates/syster-base/README.md** - Core library documentation
-- **crates/syster-cli/README.md** - CLI tool documentation  
-- **crates/syster-lsp/README.md** - LSP server documentation
-- **editors/vscode/README.md** - VS Code extension documentation
-
-## Documentation Structure
-
-### For Feature Documentation
-
-Use this structure:
-1. **Overview** - What is this feature?
-2. **Purpose** - Why does it exist?
-3. **Usage** - How to use it (with examples)
-4. **Configuration** - Available options and settings
-5. **Examples** - Real-world usage patterns
-6. **Troubleshooting** - Common issues and solutions
-
-### For Architecture Documentation
-
-Use this structure:
-1. **High-level overview** - System architecture diagram or description
-2. **Key components** - Major modules and their responsibilities
-3. **Data flow** - How information moves through the system
-4. **Design decisions** - Why things are structured this way
-5. **Constraints** - Important rules and invariants
-6. **Common operations** - How to accomplish typical tasks
-
-### For Contributing Documentation
-
-Use this structure:
-1. **Getting started** - Setup and prerequisites
-2. **Development workflow** - How to develop features
-3. **Testing guidelines** - How to write and run tests
-4. **Code conventions** - Style and patterns to follow
-5. **Pull request process** - How to submit changes
-6. **Review checklist** - What reviewers look for
-
-## Markdown Style Guide
-
-### Headers
-```markdown
-# Top-level heading (only one per document)
-
-## Section heading
-
-### Subsection heading
-
-#### Minor section (use sparingly)
-```
-
-### Code Blocks
-Always specify the language for syntax highlighting:
-
-````markdown
-```rust
-pub fn example() -> Result<(), Error> {
-    // Code here
-}
-```
-
-```bash
-cargo build
-cargo test
-```
-````
-
-### Links
-- Use descriptive link text: `[ARCHITECTURE.md](ARCHITECTURE.md)`
-- Not: `[click here](ARCHITECTURE.md)`
-- Prefer relative links within the repository
-- Use absolute links for external resources
-
-### Lists
-```markdown
-- Unordered lists use dashes
-- Keep items parallel in structure
-- Use bullet points for related items
-
-1. Ordered lists use numbers
-2. Use for sequential steps
-3. Keep numbering consistent
-```
-
-### Emphasis
-- Use **bold** for important terms and commands
-- Use *italics* for emphasis
-- Use `code formatting` for:
-  - File names and paths
-  - Commands and CLI arguments
-  - Function and variable names
-  - Code snippets inline
-
-### Tables
-```markdown
-| Feature | Status | Notes |
-|---------|--------|-------|
-| Parsing | ✅ Complete | Full grammar support |
-| LSP | ✅ Complete | All major features |
-```
-
-### Admonitions
-Use consistent symbols for different message types:
-
-```markdown
-✅ **Good:** This is a good practice
-
-❌ **Don't:** This is a bad practice
-
-⚠️ **Warning:** This is important to know
-
-💡 **Tip:** This is a helpful suggestion
-
-📝 **Note:** This is additional information
-```
-
-## Documentation Updates
-
-### When to Update Documentation
-
-**Always update docs when:**
-- Adding a new feature or API
-- Changing existing behavior
-- Adding new configuration options
-- Modifying build or test commands
-- Changing architecture or design patterns
-- Fixing bugs that users might encounter
-
-**Where to update:**
-- **README.md** - For user-facing changes
-- **ARCHITECTURE.md** - For design pattern changes
-- **CONTRIBUTING.md** - For workflow changes
-- **Doc comments** - For API changes
-- **Changelog** - For all notable changes
-
-### Documentation Review Checklist
-
-Before committing documentation changes:
-- [ ] Spell check completed
-- [ ] Grammar checked
-- [ ] Links tested (especially relative links)
-- [ ] Code examples tested and working
-- [ ] Consistent with existing style
-- [ ] No broken markdown formatting
-- [ ] Clear and concise
-- [ ] Actionable with concrete examples
-
-## Rust Doc Comments
-
-### Module Documentation
-```rust
-//! # Module Name
-//!
-//! Brief description of the module's purpose.
-//!
-//! ## Overview
-//! More detailed explanation...
-//!
-//! ## Examples
-//! ```
-//! use syster::module::Function;
-//! 
-//! let result = Function::new();
-//! ```
-```
-
-### Function Documentation
-```rust
-/// Resolves a qualified name to its symbol definition.
-///
-/// # Arguments
-///
-/// * `qualified_name` - Fully qualified name like "Package::Element"
-///
-/// # Returns
-///
-/// The symbol if found, or `None` if not found.
-///
-/// # Examples
-///
-/// ```
-/// let symbol = resolver.resolve_qualified("MyPackage::MyClass");
-/// ```
-///
-/// # Errors
-///
-/// Returns `SemanticError::UndefinedSymbol` if the name cannot be resolved.
-pub fn resolve_qualified(&self, name: &str) -> Result<&Symbol, SemanticError> {
-    // Implementation
-}
-```
-
-### What to Document
-✅ **Do document:**
-- Public APIs (functions, structs, enums)
-- Complex algorithms or non-obvious logic
-- Error conditions and edge cases
-- Invariants and preconditions
-- Examples for non-trivial usage
-
-❌ **Don't document:**
-- Self-explanatory code
-- Trivial getters/setters
-- Private implementation details (unless complex)
-- Test functions (unless testing pattern is complex)
-
-## Examples and Code Snippets
-
-### In README.md
-- Show the most common use cases first
-- Include complete, runnable examples
-- Show both simple and advanced usage
-- Include output or expected results
-
-### In ARCHITECTURE.md
-- Use pseudocode for abstract concepts
-- Use actual code for concrete implementations
-- Include before/after examples for design patterns
-- Show both good and bad examples
-
-### In CONTRIBUTING.md
-- Show complete workflows, not just fragments
-- Include all necessary commands
-- Explain why, not just how
-- Provide troubleshooting steps
-
-## Keeping Documentation Current
-
-### During Development
-- Update docs as you write code, not after
-- Make doc updates part of your PR
-- Update examples when APIs change
-- Run `cargo doc` to check doc comments
-
-### During Code Review
-- Review doc changes as carefully as code changes
-- Ensure examples compile and work
-- Check that changes are reflected in all relevant docs
-- Verify links and references are correct
-
-### Periodic Audits
-- Review documentation quarterly
-- Remove outdated information
-- Update examples with current best practices
-- Consolidate or reorganize as needed
-
-## Special Documentation Types
-
-### API Documentation
-- Generated from Rust doc comments
-- Run `cargo doc --open` to view
-- Should include examples and error conditions
-- Links to related functions and types
-
-### Tutorial Documentation
-- Step-by-step guides
-- Start simple, gradually increase complexity
-- Include complete working examples
-- Explain concepts before showing code
-
-### Reference Documentation
-- Comprehensive coverage of all features
-- Organized by category or module
-- Include all options and parameters
-- Link to examples and tutorials
-
-## Documentation Tools
-
-### Checking Documentation
-```bash
-# Build and check Rust docs
-cargo doc --no-deps --document-private-items
-
-# Check for broken links in Rust docs
-cargo doc --no-deps
-
-# Spell check (if installed)
-typos
-
-# Markdown linting (if installed)
-markdownlint **/*.md
-```
-
-### Generating Documentation
-```bash
-# Generate and open Rust API docs
-cargo doc --open
-
-# Generate docs for all crates
-cargo doc --workspace
-```
-
-## Writing Style
-
-### Voice and Tone
-- Use active voice: "The parser generates..." not "The AST is generated by..."
-- Be direct and concise
-- Use present tense: "The function returns..." not "The function will return..."
-- Be friendly but professional
-
-### Technical Accuracy
-- Be precise with terminology
-- Use consistent names for concepts
-- Define domain-specific terms
-- Link to definitions when introducing terms
-
-### Audience Awareness
-- **README.md** - Assumes basic knowledge, shows what's possible
-- **CONTRIBUTING.md** - Assumes developer familiarity with Rust
-- **ARCHITECTURE.md** - Assumes developer working on the codebase
-- **SYSML_PRIMER.md** - Assumes no SysML knowledge
-
-## Common Documentation Pitfalls
-
-❌ **Don't:**
-- Let documentation get out of sync with code
-- Use vague language like "usually" or "might"
-- Assume readers know internal terminology
-- Skip examples for complex features
-- Leave broken links or outdated screenshots
-- Write documentation after the code is done
-
-✅ **Do:**
-- Update docs with every code change
-- Be specific and concrete
-- Define terms when first used
-- Provide multiple examples for different scenarios
-- Test all links and examples
-- Write docs alongside code
-
-## Templates
-
-### New Feature Documentation Template
-```markdown
-## Feature Name
-
-### Overview
-Brief description of what the feature does.
-
-### Usage
-Basic usage example with code.
-
-### Configuration
-Available settings and their defaults.
-
-### Examples
-#### Example 1: Basic Usage
-Code and explanation.
-
-#### Example 2: Advanced Usage
-Code and explanation.
-
-### Troubleshooting
-Common issues and solutions.
-```
-
-### API Reference Template
-```rust
-/// Brief one-line description.
-///
-/// More detailed explanation of what this does,
-/// including any important behavior or edge cases.
-///
-/// # Arguments
-///
-/// * `param1` - Description of first parameter
-/// * `param2` - Description of second parameter
-///
-/// # Returns
-///
-/// Description of return value.
-///
-/// # Examples
-///
-/// ```
-/// // Example usage
-/// let result = function(arg1, arg2);
-/// ```
-///
-/// # Errors
-///
-/// Description of error conditions.
-///
-/// # Panics
-///
-/// Description of panic conditions (if any).
-pub fn function(param1: Type1, param2: Type2) -> ReturnType {
-    // Implementation
-}
-```
diff --git a/.github/instructions/refactor-lsp.md b/.github/instructions/refactor-lsp.md
deleted file mode 100644
index f0da8fa9..00000000
--- a/.github/instructions/refactor-lsp.md
+++ /dev/null
@@ -1,183 +0,0 @@
----
-applyTo: 'crates/syster-lsp/**/*.rs'
----
-
-# LSP Backend Refactoring TODO
-
-## Goal
-Refactor `backend.rs` (590 lines) into clean, modular structure following rust-analyzer pattern.
-Target: ~100 line backend.rs, separate feature modules.
-
----
-
-## Phase 1: Move utilities to core (syster-base)
-
-### 1.1 Create text utilities module ✅ COMPLETE
-- [x] Create `crates/syster-base/src/core/text_utils.rs`
-- [x] Move `extract_word_at_cursor()` from backend.rs
-- [x] Add helper: `is_word_character()`
-- [x] Add helper: `find_word_boundaries()`
-- [x] Export from `crates/syster-base/src/core/mod.rs`
-- [x] Update backend.rs to use `syster::core::text_utils::extract_word_at_cursor`
-- [x] Run tests: `cargo test`
-- [x] BONUS: Integrated unicode-ident for proper Unicode identifier support
-- [x] All 1866 tests passing
-
-### 1.2 Create text search module  
-- [x] ~~Create `crates/syster-base/src/core/text_search.rs`~~ **SKIPPED**
-- [x] ~~Move `find_text_references()` logic (without LSP types)~~ **SKIPPED**
-- [x] ~~Define `TextMatch { line: usize, col: usize, length: usize }`~~ **SKIPPED**
-- [x] ~~Function: `find_text_occurrences(text: &str, search: &str) -> Vec<TextMatch>`~~ **SKIPPED**
-- [x] ~~Export from `crates/syster-base/src/core/mod.rs`~~ **SKIPPED**
-- [x] ~~Update backend.rs to use core text search + convert to LSP Location~~ **SKIPPED**
-- [x] ~~Run tests: `cargo test`~~ **SKIPPED**
-
-**Decision**: Keep text search in backend.rs as-is. LSP features only work on valid syntax.
-This is simpler and more accurate. Can revisit if error-resilient parsing is needed later.
-
----
-
-## Phase 2: Move AST utilities to language module
-
-### 2.1 Create syntax query module
-- [ ] Create `crates/syster-base/src/language/sysml/syntax/query.rs`
-- [ ] Move `find_element_at_position()` from backend.rs
-- [ ] Make it return `Option<(String, Span)>` (remove LSP dependency)
-- [ ] Export from `crates/syster-base/src/language/sysml/syntax/mod.rs`
-- [ ] Update backend.rs to use `syster::language::sysml::syntax::query::find_element_at_position`
-- [ ] Run tests: `cargo test`
-
----
-
-## Phase 3: Create LSP feature modules (within syster-lsp)
-
-### 3.1 Create conversions module
-- [ ] Create `crates/syster-lsp/src/conversions.rs`
-- [ ] Move `span_to_lsp_range()` from backend.rs
-- [ ] Add `lsp_position_to_core()` helper
-- [ ] Add `text_match_to_location()` helper
-- [ ] Export from `crates/syster-lsp/src/lib.rs` (if exists) or main.rs
-
-### 3.2 Create hover feature module
-- [ ] Create `crates/syster-lsp/src/features/mod.rs`
-- [ ] Create `crates/syster-lsp/src/features/hover.rs`
-- [ ] Move from backend.rs:
-  - `format_rich_hover()`
-  - `format_symbol_declaration()`
-  - `get_symbol_relationships()`
-- [ ] Function: `get_hover_info(workspace, file_path, position, document_texts) -> Option<String>`
-- [ ] Run tests: `cargo test`
-
-### 3.3 Create navigation feature module
-- [ ] Create `crates/syster-lsp/src/features/navigation.rs`
-- [ ] Extract from `get_definition()`:
-  - Function: `find_symbol_definition(workspace, file_path, position, document_texts) -> Option<(PathBuf, Span)>`
-- [ ] Extract from `get_references()`:
-  - Function: `find_symbol_references(workspace, symbol_name, document_texts, include_declaration) -> Vec<(PathBuf, usize, usize)>`
-- [ ] Run tests: `cargo test`
-
-### 3.4 Create search feature module
-- [ ] Create `crates/syster-lsp/src/features/search.rs`
-- [ ] Function: `find_symbol_at_position(workspace, file_path, position) -> Option<(String, Span)>`
-- [ ] Function: `lookup_symbol_with_fallback(workspace, name) -> Option<&Symbol>`
-- [ ] Run tests: `cargo test`
-
----
-
-## Phase 4: Create LSP handlers (protocol layer)
-
-### 4.1 Create handlers module structure
-- [ ] Create `crates/syster-lsp/src/handlers/mod.rs`
-- [ ] Create `crates/syster-lsp/src/handlers/hover.rs`
-- [ ] Create `crates/syster-lsp/src/handlers/definition.rs`
-- [ ] Create `crates/syster-lsp/src/handlers/references.rs`
-
-### 4.2 Implement hover handler
-- [ ] Move hover LSP logic from `backend.get_hover()` to `handlers/hover.rs`
-- [ ] Function: `handle_hover(backend: &Backend, uri: &Url, position: Position) -> Option<Hover>`
-- [ ] Use `features::hover::get_hover_info()` + `conversions::span_to_lsp_range()`
-- [ ] Update `main.rs` to call handler
-- [ ] Run tests: `cargo test`
-
-### 4.3 Implement definition handler  
-- [ ] Move definition LSP logic from `backend.get_definition()` to `handlers/definition.rs`
-- [ ] Function: `handle_goto_definition(backend: &Backend, uri: &Url, position: Position) -> Option<Location>`
-- [ ] Use `features::navigation::find_symbol_definition()` + conversions
-- [ ] Update `main.rs` to call handler
-- [ ] Run tests: `cargo test`
-
-### 4.4 Implement references handler
-- [ ] Move references LSP logic from `backend.get_references()` to `handlers/references.rs`
-- [ ] Function: `handle_references(backend: &Backend, uri: &Url, position: Position, include_decl: bool) -> Option<Vec<Location>>`
-- [ ] Use `features::navigation::find_symbol_references()` + conversions
-- [ ] Update `main.rs` to call handler
-- [ ] Run tests: `cargo test`
-
----
-
-## Phase 5: Simplify Backend
-
-### 5.1 Clean up backend.rs
-- [ ] Remove all moved functions
-- [ ] Keep only:
-  - `struct Backend` with state (workspace, parse_errors, document_texts)
-  - `new()`
-  - `workspace()` accessor
-  - `parse_and_update()`
-  - `open_document()`, `change_document()`, `close_document()`
-  - `get_diagnostics()`
-- [ ] Target: ~100 lines
-- [ ] Run tests: `cargo test`
-
-### 5.2 Update main.rs
-- [ ] Import handlers: `use handlers::{hover, definition, references}`
-- [ ] Update `hover()` to call `hover::handle_hover()`
-- [ ] Update `goto_definition()` to call `definition::handle_goto_definition()`
-- [ ] Update `references()` to call `references::handle_references()`
-- [ ] Run tests: `cargo test`
-
----
-
-## Phase 6: Final cleanup
-
-### 6.1 Update tests
-- [ ] Move tests from `backend/tests.rs` to appropriate feature test files:
-  - `features/hover/tests.rs`
-  - `features/navigation/tests.rs`
-  - `features/search/tests.rs`
-- [ ] Keep integration-style tests in `backend/tests.rs`
-- [ ] Run all tests: `cargo test`
-
-### 6.2 Documentation
-- [ ] Add module-level docs to each new module
-- [ ] Update ARCHITECTURE.md with new structure
-- [ ] Run `cargo doc` to verify
-
-### 6.3 Final validation
-- [ ] Run `cargo clippy`
-- [ ] Run `cargo fmt`
-- [ ] Run full test suite: `cargo test`
-- [ ] Verify line counts:
-  - `backend.rs`: ~100 lines
-  - Total LSP crate: more organized, similar total lines
-- [ ] Commit: "refactor: Restructure LSP into modular architecture"
-
----
-
-## Success Criteria
-
-- [x] All tests passing
-- [x] No clippy warnings
-- [x] `backend.rs` < 150 lines
-- [x] Clear separation: core utils / language utils / LSP features / LSP protocol
-- [x] Each module has focused responsibility
-- [x] IDE features can be tested without LSP protocol
-
----
-
-## Notes
-
-- Work incrementally - test after each phase
-- Keep all tests passing throughout
-- Each phase should be a separate commit
-- Follow the chore.md checklist after each phase
diff --git a/.github/instructions/vscode-extension.md b/.github/instructions/vscode-extension.md
deleted file mode 100644
index fa13c72b..00000000
--- a/.github/instructions/vscode-extension.md
+++ /dev/null
@@ -1,227 +0,0 @@
----
-applyTo: 'editors/vscode/**/*.{ts,js,json}'
----
-
-# VS Code Extension Development Instructions
-
-## Extension Overview
-
-The Syster VS Code extension provides IDE integration for SysML v2 and KerML languages. It communicates with the syster-lsp Language Server Protocol implementation to provide rich editing features.
-
-## Technology Stack
-
-- **Language:** TypeScript
-- **Build System:** npm, tsc (TypeScript compiler)
-- **Extension API:** VS Code Extension API
-- **LSP Client:** vscode-languageclient package
-- **Packaging:** vsce (Visual Studio Code Extension Manager)
-
-## Project Structure
-
-```
-editors/vscode/
-├── client/
-│   └── src/
-│       ├── extension.ts      # Main extension entry point
-│       ├── client.ts         # LSP client setup
-│       └── server-locator.ts # Server path detection
-├── package.json              # Extension manifest and configuration
-├── tsconfig.json            # TypeScript configuration
-└── README.md                # Extension documentation
-```
-
-## Development Guidelines
-
-### VS Code Extension Best Practices
-
-1. **Activation Events**
-   - Use precise activation events to minimize extension load time
-   - Current activation: on SysML/KerML file opening
-   - Don't activate on VS Code startup unless absolutely necessary
-
-2. **Configuration**
-   - All user-facing settings should be in `package.json` under `contributes.configuration`
-   - Use clear setting names with the `sysml.` prefix
-   - Provide sensible defaults
-   - Document each setting clearly
-
-3. **Language Server Integration**
-   - Use `vscode-languageclient` for LSP communication
-   - Handle server crashes and restarts gracefully
-   - Provide user feedback for server status
-   - Support custom server path configuration for development
-
-4. **Error Handling**
-   - Catch and log all errors appropriately
-   - Show user-friendly error messages for critical failures
-   - Don't crash the extension on recoverable errors
-   - Use VS Code's output channel for detailed logs
-
-### TypeScript Guidelines
-
-```typescript
-// ✅ Good: Use async/await for asynchronous operations
-async function startServer(): Promise<void> {
-    try {
-        await client.start();
-    } catch (error) {
-        vscode.window.showErrorMessage(`Failed to start LSP: ${error}`);
-    }
-}
-
-// ✅ Good: Use proper TypeScript types
-interface ServerConfig {
-    stdlibEnabled: boolean;
-    stdlibPath: string | undefined;
-}
-
-// ✅ Good: Use VS Code API properly
-const config = vscode.workspace.getConfiguration('syster');
-const enabled = config.get<boolean>('stdlib.enabled', true);
-
-// ❌ Bad: Don't use 'any' type
-const config: any = vscode.workspace.getConfiguration(); // Don't do this
-
-// ❌ Bad: Don't ignore errors silently
-client.start().catch(() => {}); // Don't do this
-```
-
-### Extension Configuration
-
-Current extension settings (in `package.json`):
-- `syster.stdlib.enabled` - Enable/disable standard library loading
-- `syster.stdlib.path` - Custom path to standard library files
-- `syster.lsp.path` - Custom path to syster-lsp server binary
-- `syster.lsp.trace.server` - Trace LSP communication for debugging
-
-### Testing the Extension
-
-```bash
-# Install dependencies
-cd editors/vscode
-npm install
-
-# Compile TypeScript
-npm run compile
-
-# Watch mode for development
-npm run watch
-
-# Package the extension
-npm run package
-```
-
-To test locally:
-1. Open the `editors/vscode` folder in VS Code
-2. Press F5 to launch Extension Development Host
-3. Open a `.sysml` or `.kerml` file to activate the extension
-4. Check "Output" panel → "Syster LSP" for logs
-
-### Build & Deployment
-
-```bash
-# Compile TypeScript
-npm run compile
-
-# Package extension (.vsix file)
-npm run package
-
-# Install locally for testing
-code --install-extension syster-*.vsix
-```
-
-### Code Organization
-
-- **client/src/extension.ts** - Main entry point with `activate()` and `deactivate()`
-- **client/src/client.ts** - LSP client setup and configuration
-- **client/src/server-locator.ts** - Server binary path detection
-- Keep extension logic simple - delegate to LSP server
-- Configuration management should be centralized
-- Use VS Code's workspace configuration API
-
-### Common Tasks
-
-**Adding a new configuration setting:**
-1. Add to `contributes.configuration` in `package.json` with `syster.` prefix
-2. Document with clear description and default value
-3. Read in extension code using `vscode.workspace.getConfiguration('syster')`
-4. Pass to LSP server if needed via initialization options
-
-**Adding a new command:**
-1. Define in `contributes.commands` in `package.json`
-2. Register in `extension.ts` with `vscode.commands.registerCommand()`
-3. Add to activation events if needed
-
-**Updating LSP client:**
-1. Modify initialization options in `extension.ts`
-2. Ensure server supports the new options
-3. Test communication between client and server
-
-### Debugging
-
-Enable detailed logs:
-```typescript
-// In extension.ts, add to client options:
-const clientOptions: LanguageClientOptions = {
-    outputChannel: window.createOutputChannel('Syster LSP'),
-    traceOutputChannel: window.createOutputChannel('Syster LSP Trace'),
-};
-```
-
-Check logs in:
-- Output panel → "Syster LSP" (general logs)
-- Output panel → "Syster LSP Trace" (detailed protocol trace)
-
-### Performance Considerations
-
-- Minimize synchronous operations in activation
-- Use lazy initialization where possible
-- Avoid blocking the main extension thread
-- Let the LSP server handle expensive computations
-
-### Security
-
-- Don't bundle sensitive data or credentials
-- Validate all user-provided paths before using
-- Use VS Code's secure storage API for any secrets
-- Don't execute arbitrary user-provided code
-
-### Integration with syster-lsp
-
-The extension communicates with `crates/syster-lsp/` which provides:
-- Document synchronization
-- Diagnostics (parse errors)
-- Code completion
-- Go to definition
-- Find references
-- Hover information
-- Symbol outline
-- Code formatting
-- Rename symbol
-- Semantic tokens (syntax highlighting)
-- Inlay hints
-- Folding ranges
-- Selection ranges
-
-Ensure the extension properly:
-1. Starts and stops the server lifecycle
-2. Handles server crashes/restarts
-3. Passes configuration to server
-4. Displays diagnostics to user
-5. Registers all supported LSP features
-
-## VS Code Extension Manifest
-
-Key sections in `package.json`:
-- `engines.vscode` - Minimum VS Code version
-- `activationEvents` - When to activate the extension
-- `contributes.languages` - Language definitions (SysML, KerML)
-- `contributes.grammars` - TextMate grammars for syntax highlighting
-- `contributes.configuration` - Extension settings
-- `main` - Entry point file
-
-## Related Documentation
-
-- [VS Code Extension API](https://code.visualstudio.com/api)
-- [Language Server Protocol](https://microsoft.github.io/language-server-protocol/)
-- [vscode-languageclient](https://github.com/microsoft/vscode-languageserver-node)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8322353a..a0a5787f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,6 @@
 # Meta-repo CI workflow
 # This repo is a meta-repository that aggregates submodules.
-# Each submodule (syster-base, syster-cli, syster-lsp) has its own CI.
+# Each submodule has its own CI workflow.
 # This workflow validates that submodules are properly configured.
 
 name: CI
@@ -26,12 +26,15 @@ jobs:
           git submodule status
           echo "All submodules are properly configured."
       
-      - name: Validate Cargo.toml
+      - name: Validate structure
         run: |
-          echo "Checking Cargo.toml..."
-          if grep -q 'members = \[\]' Cargo.toml; then
-            echo "✓ Meta-repo workspace configured correctly (no members)"
-          else
-            echo "✗ Expected meta-repo with no workspace members"
-            exit 1
-          fi
+          echo "Checking repository structure..."
+          for dir in base cli language-server language-client modeller viewer diagram-core diagram-ui pipelines; do
+            if [ -d "$dir" ]; then
+              echo "✓ $dir exists"
+            else
+              echo "✗ $dir missing"
+              exit 1
+            fi
+          done
+          echo "All expected directories present."
diff --git a/.github/workflows/copilot-auto-retry.yml b/.github/workflows/copilot-auto-retry.yml
deleted file mode 100644
index 093071c6..00000000
--- a/.github/workflows/copilot-auto-retry.yml
+++ /dev/null
@@ -1,102 +0,0 @@
-name: Auto-notify Copilot on CI Failure
-
-on:
-  workflow_run:
-    workflows: ["CI"]
-    types: [completed]
-
-jobs:
-  notify-copilot:
-    if: github.event.workflow_run.conclusion == 'failure' && github.event.workflow_run.event == 'pull_request'
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-      actions: read
-      contents: read
-    
-    steps:
-      - name: Get PR number
-        id: pr
-        uses: actions/github-script@v7
-        with:
-          script: |
-            try {
-              const pulls = await github.rest.pulls.list({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                head: `${github.event.workflow_run.head_repository.owner.login}:${github.event.workflow_run.head_branch}`,
-                state: 'open'
-              });
-              
-              if (pulls.data.length === 0) {
-                console.log('No open PR found for this branch');
-                return 'none';
-              }
-              
-              return pulls.data[0].number.toString();
-            } catch (error) {
-              console.error('Error fetching PR:', error);
-              return 'none';
-            }
-          result-encoding: string
-      
-      - name: Check if already notified
-        if: steps.pr.outputs.result != 'none'
-        id: check-notified
-        uses: actions/github-script@v7
-        with:
-          script: |
-            try {
-              const prNumber = parseInt('${{ steps.pr.outputs.result }}');
-              const comments = await github.rest.issues.listComments({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: prNumber,
-                per_page: 5,
-                sort: 'created',
-                direction: 'desc',
-              });
-              
-              // Check if Copilot was already notified in the most recent 5 comments
-              const alreadyNotified = comments.data.some(comment => 
-                comment.body.includes('@copilot') && 
-                comment.body.includes('CI pipeline failed')
-              );
-              
-              return alreadyNotified ? 'true' : 'false';
-            } catch (error) {
-              console.error('Error checking for duplicate notifications:', error);
-              return 'false';
-            }
-          result-encoding: string
-      
-      - name: Get workflow run logs URL
-        if: steps.pr.outputs.result != 'none' && steps.check-notified.outputs.result == 'false'
-        id: logs
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const runId = github.event.workflow_run.id;
-            const url = `https://github.com/${context.repo.owner}/${context.repo.repo}/actions/runs/${runId}`;
-            return url;
-          result-encoding: string
-      
-      - name: Comment on PR
-        if: steps.pr.outputs.result != 'none' && steps.check-notified.outputs.result == 'false'
-        uses: actions/github-script@v7
-        with:
-          script: |
-            try {
-              const prNumber = parseInt('${{ steps.pr.outputs.result }}');
-              const logsUrl = '${{ steps.logs.outputs.result }}';
-              
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: prNumber,
-                body: `@copilot The CI pipeline failed. Please analyze the errors and fix the issues.\n\n📋 [View failed workflow run](${logsUrl})`
-              });
-            } catch (error) {
-              console.error('Error posting comment:', error);
-              throw error;
-            }
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 7dc3465a..7ac8cfc0 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -37,6 +37,7 @@ jobs:
           echo "version=$VERSION" >> $GITHUB_OUTPUT
           echo "Release version: $VERSION"
 
+      # Rust binaries
       - name: Download syster-lsp binaries
         uses: dawidd6/action-download-artifact@v3
         with:
@@ -61,6 +62,68 @@ jobs:
           search_artifacts: true
         continue-on-error: true
 
+      # VS Code extensions
+      - name: Download language-client extension
+        uses: dawidd6/action-download-artifact@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repo: jade-codes/syster-vscode-lsp
+          workflow: ci.yml
+          branch: main
+          name: vsix-*
+          path: artifacts/language-client
+          search_artifacts: true
+        continue-on-error: true
+
+      - name: Download modeller extension
+        uses: dawidd6/action-download-artifact@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repo: jade-codes/syster-vscode-modeller
+          workflow: ci.yml
+          branch: main
+          name: vsix-*
+          path: artifacts/modeller
+          search_artifacts: true
+        continue-on-error: true
+
+      - name: Download viewer extension
+        uses: dawidd6/action-download-artifact@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repo: jade-codes/syster-vscode-viewer
+          workflow: ci.yml
+          branch: main
+          name: vsix-*
+          path: artifacts/viewer
+          search_artifacts: true
+        continue-on-error: true
+
+      # npm packages
+      - name: Download diagram-core package
+        uses: dawidd6/action-download-artifact@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repo: jade-codes/syster-diagram-core
+          workflow: ci.yml
+          branch: main
+          name: npm-package
+          path: artifacts/diagram-core
+          search_artifacts: true
+        continue-on-error: true
+
+      - name: Download diagram-ui package
+        uses: dawidd6/action-download-artifact@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          repo: jade-codes/syster-diagram-ui
+          workflow: ci.yml
+          branch: main
+          name: npm-package
+          path: artifacts/diagram-ui
+          search_artifacts: true
+        continue-on-error: true
+
       - name: List collected artifacts
         run: |
           echo "=== Collected Artifacts ==="
@@ -68,38 +131,10 @@ jobs:
 
       - name: Package artifacts
         run: |
-          VERSION="${{ steps.version.outputs.version }}"
           mkdir -p release
           
-          # Package syster-lsp binaries
-          if [ -d "artifacts/syster-lsp" ]; then
-            for dir in artifacts/syster-lsp/binaries-*; do
-              if [ -d "$dir" ]; then
-                target=$(basename "$dir" | sed 's/binaries-//')
-                echo "Packaging syster-lsp for $target"
-                cd "$dir"
-                if [ -f "syster-lsp" ] || [ -f "syster-lsp.exe" ]; then
-                  tar -czf "../../release/syster-lsp-${VERSION}-${target}.tar.gz" *
-                fi
-                cd - > /dev/null
-              fi
-            done
-          fi
-          
-          # Package syster-cli binaries
-          if [ -d "artifacts/syster-cli" ]; then
-            for dir in artifacts/syster-cli/binaries-*; do
-              if [ -d "$dir" ]; then
-                target=$(basename "$dir" | sed 's/binaries-//')
-                echo "Packaging syster-cli for $target"
-                cd "$dir"
-                if [ -f "syster" ] || [ -f "syster.exe" ]; then
-                  tar -czf "../../release/syster-cli-${VERSION}-${target}.tar.gz" *
-                fi
-                cd - > /dev/null
-              fi
-            done
-          fi
+          # Copy all artifacts to release folder
+          find artifacts -type f \( -name "*.tar.gz" -o -name "*.zip" -o -name "*.vsix" -o -name "*.tgz" \) -exec cp {} release/ \; 2>/dev/null || true
           
           ls -la release/ || echo "No packages created"
 
@@ -141,13 +176,28 @@ jobs:
           body: |
             ## Syster ${{ steps.version.outputs.version }}
             
-            This release includes:
+            This release includes all Syster components:
+            
+            ### Binaries
             - **syster-cli**: Command-line tool for SysML v2 analysis
             - **syster-lsp**: Language Server Protocol implementation
             
+            ### VS Code Extensions
+            - **syster-lsp**: Language support (syntax, diagnostics, completion)
+            - **syster-modeller**: Visual diagram editor
+            - **syster-viewer**: Read-only diagram viewer
+            
+            ### npm Packages
+            - **@syster/diagram-core**: Diagram types and layout utilities
+            - **@syster/diagram-ui**: React Flow diagram components
+            
             ### Installation
             
-            Download the appropriate binary for your platform and extract it.
+            **CLI/LSP**: Download the appropriate binary for your platform and extract it.
+            
+            **VS Code Extensions**: Install the `.vsix` files via `Extensions: Install from VSIX...`
+            
+            **npm Packages**: `npm install @syster/diagram-core @syster/diagram-ui`
             
             ### Platforms
             - Linux (x86_64)
diff --git a/.gitmodules b/.gitmodules
index ed2bf4c9..7b02c25e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,27 +1,27 @@
-[submodule "crates/syster-base"]
-	path = crates/syster-base
+[submodule "pipelines"]
+	path = pipelines
+	url = https://github.com/jade-codes/syster-pipelines.git
+[submodule "base"]
+	path = base
 	url = https://github.com/jade-codes/syster-base.git
-[submodule "crates/syster-cli"]
-	path = crates/syster-cli
+[submodule "cli"]
+	path = cli
 	url = https://github.com/jade-codes/syster-cli.git
-[submodule "crates/syster-lsp"]
-	path = crates/syster-lsp
+[submodule "language-server"]
+	path = language-server
 	url = https://github.com/jade-codes/syster-lsp.git
-[submodule "packages/diagram-core"]
-	path = packages/diagram-core
+[submodule "language-client"]
+	path = language-client
+	url = https://github.com/jade-codes/syster-vscode-lsp.git
+[submodule "diagram-core"]
+	path = diagram-core
 	url = https://github.com/jade-codes/syster-diagram-core.git
-[submodule "packages/diagram-ui"]
-	path = packages/diagram-ui
+[submodule "diagram-ui"]
+	path = diagram-ui
 	url = https://github.com/jade-codes/syster-diagram-ui.git
-[submodule "editors/vscode-viewer"]
-	path = editors/vscode-viewer
-	url = https://github.com/jade-codes/syster-vscode-viewer.git
-[submodule "editors/vscode-modeller"]
-	path = editors/vscode-modeller
+[submodule "modeller"]
+	path = modeller
 	url = https://github.com/jade-codes/syster-vscode-modeller.git
-[submodule "pipelines"]
-	path = pipelines
-	url = https://github.com/jade-codes/syster-pipelines.git
-[submodule "editors/vscode-lsp"]
-	path = editors/vscode-lsp
-	url = https://github.com/jade-codes/syster-vscode-lsp.git
+[submodule "viewer"]
+	path = viewer
+	url = https://github.com/jade-codes/syster-vscode-viewer.git
diff --git a/Cargo.lock b/Cargo.lock
deleted file mode 100644
index 04bbadad..00000000
--- a/Cargo.lock
+++ /dev/null
@@ -1,919 +0,0 @@
-# This file is automatically @generated by Cargo.
-# It is not intended for manual editing.
-version = 4
-
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-
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-name = "version_check"
-version = "0.9.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
-
-[[package]]
-name = "void"
-version = "1.0.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6a02e4885ed3bc0f2de90ea6dd45ebcbb66dacffe03547fadbb0eeae2770887d"
-
-[[package]]
-name = "wasip2"
-version = "1.0.1+wasi-0.2.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0562428422c63773dad2c345a1882263bbf4d65cf3f42e90921f787ef5ad58e7"
-dependencies = [
- "wit-bindgen",
-]
-
-[[package]]
-name = "windows-link"
-version = "0.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0805222e57f7521d6a62e36fa9163bc891acd422f971defe97d64e70d0a4fe5"
-
-[[package]]
-name = "windows-sys"
-version = "0.61.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae137229bcbd6cdf0f7b80a31df61766145077ddf49416a728b02cb3921ff3fc"
-dependencies = [
- "windows-link",
-]
-
-[[package]]
-name = "winnow"
-version = "0.7.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a5364e9d77fcdeeaa6062ced926ee3381faa2ee02d3eb83a5c27a8825540829"
-dependencies = [
- "memchr",
-]
-
-[[package]]
-name = "wit-bindgen"
-version = "0.46.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f17a85883d4e6d00e8a97c586de764dabcc06133f7f1d55dce5cdc070ad7fe59"
diff --git a/Cargo.toml b/Cargo.toml
deleted file mode 100644
index b30703e0..00000000
--- a/Cargo.toml
+++ /dev/null
@@ -1,159 +0,0 @@
-# Syster Meta-Repository
-# This workspace aggregates all Syster Rust crates via git submodules.
-# Each crate lives in its own repository for independent development and versioning.
-#
-# Note: Each crate is an independent project with its own Cargo.toml.
-# Build each crate separately:
-#   cd crates/syster-base && cargo build
-#   cd crates/syster-cli && cargo build
-#   cd crates/syster-lsp && cargo build
-
-[workspace]
-members = []
-exclude = [
-    "crates/syster-base",
-    "crates/syster-cli",
-    "crates/syster-lsp",
-]
-resolver = "2"
-
-[workspace.package]
-version = "0.1.0"
-edition = "2024"
-authors = ["jade-codes"]
-license = "MIT"
-repository = "https://github.com/jade-codes/syster"
-
-[workspace.lints.clippy]
-# Enforce explicit error handling
-unwrap_used = "warn"
-expect_used = "warn"
-panic = "warn"
-todo = "warn"
-unimplemented = "warn"
-
-# Code quality
-dbg_macro = "warn"
-print_stdout = "warn"
-print_stderr = "warn"
-missing_errors_doc = "warn"
-missing_panics_doc = "warn"
-
-# Performance
-inefficient_to_string = "warn"
-unnecessary_wraps = "warn"
-
-# Style consistency
-enum_glob_use = "warn"
-wildcard_imports = "warn"
-
-# Test quality - deny control flow complexity in tests
-collapsible_if = "warn"
-collapsible_else_if = "warn"
-cognitive_complexity = "deny"
-
-# Deny by category (set explicit priority to avoid ambiguity)
-correctness = { level = "deny", priority = -1 }
-suspicious = { level = "deny", priority = -1 }
-complexity = { level = "deny", priority = -1 }
-perf = { level = "deny", priority = -1 }
-
-# ============================================================================
-# Build Optimization Profiles
-# ============================================================================
-
-# Dev profile: optimize for fast compile times
-[profile.dev]
-opt-level = 0
-debug = true
-incremental = true
-# More codegen units = faster compile, slower runtime (fine for dev)
-codegen-units = 256
-
-# Dev dependencies can be optimized (tests run faster)
-[profile.dev.package."*"]
-opt-level = 1
-
-# Test profile inherits from dev but can have overrides
-# Using opt-level = 1 for faster tests while keeping debug info
-[profile.test]
-opt-level = 1
-debug = true
-incremental = true
-
-# Optimize parsing dependencies in test builds for faster tests
-[profile.test.package.pest]
-opt-level = 3
-
-[profile.test.package.pest_derive]
-opt-level = 3
-
-[profile.test.package.pest_meta]
-opt-level = 3
-
-[profile.test.package.pest_generator]
-opt-level = 3
-
-# Also optimize in dev builds
-[profile.dev.package.pest]
-opt-level = 3
-
-[profile.dev.package.pest_derive]
-opt-level = 3
-
-[profile.dev.package.pest_meta]
-opt-level = 3
-
-[profile.dev.package.pest_generator]
-opt-level = 3
-
-# Optimize other parsing/syntax dependencies
-[profile.dev.package.rowan]
-opt-level = 3
-
-[profile.dev.package.logos]
-opt-level = 3
-
-[profile.dev.package.from-pest]
-opt-level = 3
-
-[profile.dev.package.pest-ast]
-opt-level = 3
-
-[profile.dev.package.rayon]
-opt-level = 3
-
-[profile.dev.package.rayon-core]
-opt-level = 3
-
-[profile.test.package.rowan]
-opt-level = 3
-
-[profile.test.package.logos]
-opt-level = 3
-
-[profile.test.package.from-pest]
-opt-level = 3
-
-[profile.test.package.pest-ast]
-opt-level = 3
-
-[profile.test.package.rayon]
-opt-level = 3
-
-[profile.test.package.rayon-core]
-opt-level = 3
-
-# Release profile: balanced for dev containers (lower memory usage)
-[profile.release]
-opt-level = 3
-lto = false
-codegen-units = 16
-strip = true
-
-# Production profile: maximum optimization (use with `cargo build --profile production`)
-# Requires more memory - may fail in constrained environments
-[profile.production]
-inherits = "release"
-lto = "thin"
-codegen-units = 1
diff --git a/README.md b/README.md
index 953c1fd2..b91d7277 100644
--- a/README.md
+++ b/README.md
@@ -4,38 +4,72 @@
 
 A Rust-based parser and tooling for SysML v2 (Systems Modeling Language) and KerML (Kernel Modeling Language).
 
-## Meta-Repository Structure
-
-This is a **meta-repository** that aggregates all Syster components via Git submodules. Each component lives in its own repository for independent development and versioning.
-
-### Rust Crates
-
-| Component | Repository | Description |
-|-----------|------------|-------------|
-| **syster-base** | [jade-codes/syster-base](https://github.com/jade-codes/syster-base) | Core library with parser, AST, and semantic analysis |
-| **syster-cli** | [jade-codes/syster-cli](https://github.com/jade-codes/syster-cli) | Command-line tool for analyzing SysML/KerML files |
-| **syster-lsp** | [jade-codes/syster-lsp](https://github.com/jade-codes/syster-lsp) | Language Server Protocol implementation with VS Code extension |
-
-### TypeScript Packages
+## Architecture
+
+```mermaid
+graph TB
+    subgraph "SysML v2 Files"
+        SysML[".sysml / .kerml"]
+    end
+
+    subgraph "Core (Rust)"
+        Base[base<br/>Parser, AST, Semantic Analysis]
+        CLI[cli<br/>Command Line Tool]
+        LSP[language-server<br/>LSP Implementation]
+    end
+
+    subgraph "VS Code Extensions (TypeScript)"
+        Client[language-client<br/>LSP Extension]
+        Modeller[modeller<br/>Diagram Editor]
+        Viewer[viewer<br/>Diagram Viewer]
+    end
+
+    subgraph "Diagram Library (TypeScript)"
+        Core[diagram-core<br/>Types & Layout]
+        UI[diagram-ui<br/>React Components]
+    end
+
+    SysML --> Base
+    Base --> CLI
+    Base --> LSP
+    LSP <--> Client
+    Core --> UI
+    UI --> Modeller
+    UI --> Viewer
+    Client --> Modeller
+    Client --> Viewer
+```
 
-| Component | Repository | Description |
-|-----------|------------|-------------|
-| **@syster/diagram-core** | [jade-codes/syster-diagram-core](https://github.com/jade-codes/syster-diagram-core) | Core diagram types and layout algorithms |
-| **@syster/diagram-ui** | [jade-codes/syster-diagram-ui](https://github.com/jade-codes/syster-diagram-ui) | React Flow UI components for diagrams |
+## Repository Structure
 
-### VS Code Extensions
+Feature-based organization with independent submodules for versioning flexibility.
 
-| Extension | Repository | Description |
-|-----------|------------|-------------|
-| **sysml-language-support** | [jade-codes/syster-vscode-lsp](https://github.com/jade-codes/syster-vscode-lsp) | Main language support extension (LSP client) |
-| **syster-viewer** | [jade-codes/syster-vscode-viewer](https://github.com/jade-codes/syster-vscode-viewer) | Diagram viewer extension |
-| **syster-modeller** | [jade-codes/syster-vscode-modeller](https://github.com/jade-codes/syster-vscode-modeller) | Diagram modeller extension |
+```
+syster/
+├── base/                  # Parser, AST, semantic analysis
+├── cli/                   # Command-line tool
+├── language-server/       # Language Server Protocol implementation
+├── language-client/       # VS Code LSP extension
+├── modeller/              # VS Code modeller extension
+├── viewer/                # VS Code viewer extension
+├── diagram-core/          # Diagram types and layout (TypeScript)
+├── diagram-ui/            # React Flow components (TypeScript)
+└── pipelines/             # CI/CD pipeline templates
+```
 
-### Infrastructure
+### Components
 
-| Component | Repository | Description |
-|-----------|------------|-------------|
-| **syster-pipelines** | [jade-codes/syster-pipelines](https://github.com/jade-codes/syster-pipelines) | CI/CD pipeline templates |
+| Feature | Path | Repository | Description |
+|---------|------|------------|-------------|
+| **Base** | `base/` | [syster-base](https://github.com/jade-codes/syster-base) | Parser, AST, semantic analysis |
+| **CLI** | `cli/` | [syster-cli](https://github.com/jade-codes/syster-cli) | Command-line tool |
+| **LSP Server** | `language-server/` | [syster-lsp](https://github.com/jade-codes/syster-lsp) | Language Server Protocol |
+| **LSP Client** | `language-client/` | [syster-vscode-lsp](https://github.com/jade-codes/syster-vscode-lsp) | VS Code language support |
+| **Diagram Core** | `diagram-core/` | [syster-diagram-core](https://github.com/jade-codes/syster-diagram-core) | Diagram types (TS) |
+| **Diagram UI** | `diagram-ui/` | [syster-diagram-ui](https://github.com/jade-codes/syster-diagram-ui) | React Flow components |
+| **Modeller** | `modeller/` | [syster-vscode-modeller](https://github.com/jade-codes/syster-vscode-modeller) | VS Code modeller |
+| **Viewer** | `viewer/` | [syster-vscode-viewer](https://github.com/jade-codes/syster-vscode-viewer) | VS Code viewer |
+| **Pipelines** | `pipelines/` | [syster-pipelines](https://github.com/jade-codes/syster-pipelines) | CI/CD templates |
 
 ## Getting Started
 
@@ -48,46 +82,48 @@ This repository includes a VS Code dev container with all development tools pre-
 3. The container will automatically:
    - Initialize all git submodules
    - Install Rust, Node.js, and Bun
-   - Set up the VS Code LSP extension dependencies
+   - Set up dependencies
 
 ### Clone with Submodules
 
-\`\`\`bash
+```bash
 # Clone with all submodules
 git clone --recurse-submodules https://github.com/jade-codes/syster.git
 
 # Or if already cloned, initialize submodules
 git submodule update --init --recursive
-\`\`\`
+```
 
-### Build Rust Crates
+### Build
 
-Each crate is independent - build separately:
+Each submodule is built independently. Navigate to the submodule directory and follow its README:
 
-\`\`\`bash
-cd crates/syster-base && cargo build && cargo test
-cd crates/syster-cli && cargo build
-cd crates/syster-lsp && cargo build
-\`\`\`
+```bash
+# Build the base parser
+cd base && cargo build && cargo test
 
-### Build TypeScript Packages
+# Build the CLI
+cd cli && cargo build
 
-```bash
-cd editors/vscode-lsp && npm install && npm run esbuild
-cd packages/diagram-core && bun install
-cd packages/diagram-ui && bun install
+# Build the LSP server
+cd language-server && cargo build
+
+# Build VS Code extensions
+cd language-client && npm install && npm run compile
+cd modeller && npm install && npm run compile
+cd viewer && npm install && npm run compile
 ```
 
 ### Running the VS Code Extension Locally
 
 1. Build the LSP binary:
    ```bash
-   cd crates/syster-lsp && cargo build --release
+   cd language-server && cargo build --release
    ```
 
 2. Build the extension:
    ```bash
-   cd editors/vscode-lsp && npm install && npm run esbuild
+   cd language-client && npm install && npm run esbuild
    ```
 
 3. Press `F5` in VS Code to launch the extension in a new window
diff --git a/base b/base
new file mode 160000
index 00000000..9c4e2039
--- /dev/null
+++ b/base
@@ -0,0 +1 @@
+Subproject commit 9c4e2039cc1cca7ea52147ebadbaca354324a7c9
diff --git a/cli b/cli
new file mode 160000
index 00000000..e62fdb79
--- /dev/null
+++ b/cli
@@ -0,0 +1 @@
+Subproject commit e62fdb79c40e37f8054b11462baff6fae986a6bb
diff --git a/crates/syster-base b/crates/syster-base
deleted file mode 160000
index 3e599f30..00000000
--- a/crates/syster-base
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3e599f30f4819dfe74a58d5c2ea7ba511e0eb49c
diff --git a/crates/syster-cli b/crates/syster-cli
deleted file mode 160000
index d770065f..00000000
--- a/crates/syster-cli
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d770065f8f325afa405d2207474de5d50cc6bc19
diff --git a/crates/syster-lsp b/crates/syster-lsp
deleted file mode 160000
index 29303ad9..00000000
--- a/crates/syster-lsp
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 29303ad9266c340af9c85b1ce53bc5317c0df721
diff --git a/diagram-core b/diagram-core
new file mode 160000
index 00000000..562abd7f
--- /dev/null
+++ b/diagram-core
@@ -0,0 +1 @@
+Subproject commit 562abd7f8779ea9e474a10e70f22a7d86ca2c2c0
diff --git a/diagram-ui b/diagram-ui
new file mode 160000
index 00000000..39213fc9
--- /dev/null
+++ b/diagram-ui
@@ -0,0 +1 @@
+Subproject commit 39213fc95e1be41ff08e64c31974e93e8bf8136b
diff --git a/editors/vscode-lsp b/editors/vscode-lsp
deleted file mode 160000
index 788f0a17..00000000
--- a/editors/vscode-lsp
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 788f0a173cb8472e3eea8e245e514eed4acc8f3e
diff --git a/editors/vscode-modeller b/editors/vscode-modeller
deleted file mode 160000
index a8d2ac3c..00000000
--- a/editors/vscode-modeller
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a8d2ac3c05ed374b5afd63b30c0c7c4e24307a55
diff --git a/editors/vscode-viewer b/editors/vscode-viewer
deleted file mode 160000
index a5ca91a7..00000000
--- a/editors/vscode-viewer
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a5ca91a735295f0c0b2abb4b36e706b02432e745
diff --git a/language-client b/language-client
new file mode 160000
index 00000000..c8447b47
--- /dev/null
+++ b/language-client
@@ -0,0 +1 @@
+Subproject commit c8447b471a3fac7e803f40657e704a6519e82e20
diff --git a/language-server b/language-server
new file mode 160000
index 00000000..33734da8
--- /dev/null
+++ b/language-server
@@ -0,0 +1 @@
+Subproject commit 33734da898a810be738b6bd34e4684d2fb9b4efe
diff --git a/modeller b/modeller
new file mode 160000
index 00000000..d080a21b
--- /dev/null
+++ b/modeller
@@ -0,0 +1 @@
+Subproject commit d080a21b8b0da5f18beb495e9d11637983cddd31
diff --git a/package.json b/package.json
deleted file mode 100644
index 05939011..00000000
--- a/package.json
+++ /dev/null
@@ -1,28 +0,0 @@
-{
-  "name": "syster-meta",
-  "version": "0.1.0",
-  "private": true,
-  "description": "Syster - SysML v2 Parser and Tooling (Meta Repository). This is a meta-repository - each subdirectory is a git submodule with its own dependencies.",
-  "scripts": {
-    "postinstall": "echo 'Note: This is a meta-repo. Run npm install in individual submodules as needed.'",
-    "setup:vscode-lsp": "cd editors/vscode-lsp && npm install",
-    "setup:vscode-viewer": "cd editors/vscode-viewer && npm install",
-    "setup:vscode-modeller": "cd editors/vscode-modeller && npm install",
-    "setup:packages": "cd packages/diagram-core && bun install && cd ../diagram-ui && bun install",
-    "setup:all": "npm run setup:vscode-lsp && npm run setup:packages"
-  },
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/jade-codes/syster.git"
-  },
-  "keywords": [
-    "sysml",
-    "sysml-v2",
-    "kerml",
-    "parser",
-    "systems-engineering",
-    "modeling"
-  ],
-  "author": "jade-codes",
-  "license": "MIT"
-}
diff --git a/packages/diagram-core b/packages/diagram-core
deleted file mode 160000
index a7887de5..00000000
--- a/packages/diagram-core
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a7887de532c1fb4bb736eef41e33f3b1013bb63f
diff --git a/packages/diagram-ui b/packages/diagram-ui
deleted file mode 160000
index 702658a8..00000000
--- a/packages/diagram-ui
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 702658a8f8e40bce08e4a8d0b58cf258b02aa70d
diff --git a/viewer b/viewer
new file mode 160000
index 00000000..910fe632
--- /dev/null
+++ b/viewer
@@ -0,0 +1 @@
+Subproject commit 910fe63221b703bdea0f0b251c1f506fba213678