chore: reorganization following layout_conventions.md

.gitignore

@@ -3,11 +3,13 @@ OLD
 # Generated by Cargo
 # will have compiled files and executables
 debug/
-target/
+target
+distribution
 /dist/
 
 # Claude Code session files
 .coder/
+.claude
 
 # Generated documentation
 /target/doc/

CLAUDE.md

@@ -1,424 +0,0 @@
-# CLAUDE.md
-
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
-
-## Quick Start Commands
-
-### Build & Verification
-```bash
-just check-all          # Complete verification: fmt + lint + check + test + audit
-just check              # cargo check --all
-just build              # cargo build --all
-just build-release      # cargo build --release
-```
-
-### Testing
-```bash
-just test               # All library tests (632+ tests)
-just test-all           # Library + integration tests
-just test-verbose       # Tests with output and logging
-just test-watch         # Continuous testing on file changes
-cargo test -p <crate>   # Test specific crate (e.g., cargo test -p syntaxis-core)
-```
-
-### Code Quality
-```bash
-just fmt                # Format code (cargo fmt)
-just lint               # Lint with clippy
-just lint-pedantic      # Lint with pedantic warnings
-just audit              # Security audit
-```
-
-### Running Applications
-```bash
-just run-cli [ARGS]           # Run syntaxis CLI tool
-just run-tui                  # Run TUI application
-just run-api                  # Run REST API server (port 3000) with Leptos dashboard
-just dev-dashboard            # Dev server for Leptos dashboard (port 8080, proxies API)
-just build-dashboard          # Build Leptos WASM dashboard
-just check-dashboard-tools    # Check if dashboard prerequisites installed
-```
-
-### Installation with Presets
-
-Enhanced installer with intelligent preset selection and optional provctl integration:
-
-```bash
-# Simple local installation (default)
-nu scripts/provisioning/install-with-presets.nu
-
-# Install with specific preset
-nu scripts/provisioning/install-with-presets.nu --preset dev
-nu scripts/provisioning/install-with-presets.nu --preset staging
-nu scripts/provisioning/install-with-presets.nu --preset production
-
-# Interactive mode (will ask questions)
-nu scripts/provisioning/install-with-presets.nu --interactive
-
-# Generate configuration file
-nu scripts/provisioning/install-with-presets.nu --preset dev --generate-config > my-install.toml
-
-# Install from configuration file
-nu scripts/provisioning/install-with-presets.nu --config my-install.toml
-
-# Detect provctl availability
-nu scripts/provisioning/detect-provctl.nu --verbose
-
-# Manage services with provctl
-nu scripts/provisioning/provctl-services.nu list local
-nu scripts/provisioning/provctl-services.nu deploy dev
-nu scripts/provisioning/provctl-services.nu start surrealdb
-nu scripts/provisioning/provctl-services.nu status
-```
-
-**Installation Presets:**
-
-| Preset | Use Case | Database | Services | provctl |
-|--------|----------|----------|----------|---------|
-| `local` | Solo development | SQLite | None | ❌ Not needed |
-| `dev` | Full-stack dev | SurrealDB (server) | API, Dashboard, NATS | ✅ Recommended |
-| `staging` | CI/CD, teams | SurrealDB (docker) | All + monitoring | ✅ Recommended |
-| `production` | Enterprise | SurrealDB (K8s) | All + HA | ❌ K8s manages |
-
-**Configuration:**
-- All presets defined in `configs/installation.toml`
-- Service definitions in `configs/provisioning/services/`
-- Documentation in `docs/INSTALLATION_CONTEXTS.md`
-
-**Features:**
-- ✅ Automatic provctl detection and optional integration
-- ✅ Declarative configuration files
-- ✅ Service management (start, stop, status, deploy)
-- ✅ Interactive guided installation
-- ✅ Graceful fallback when provctl unavailable
-- ✅ Health checks for services
-
-## Architecture Overview
-
-**syntaxis** is a standalone, production-grade project management platform with multi-interface support. It's designed as the foundation for VAPORA SST (Software Specification & Tasks).
-
-### Core Components
-
-| Component | Location | Purpose | Tests | Status |
-|-----------|----------|---------|-------|--------|
-| **syntaxis-core** | `core/crates/syntaxis-core` | Core library: projects, phases, tasks, SurrealDB + SQLite persistence | 179 | ✅ Active |
-| **syntaxis-cli** | `core/crates/syntaxis-cli` | Command-line interface via clap | - | ✅ Active |
-| **syntaxis-tui** | `core/crates/syntaxis-tui` | Terminal UI via ratatui, vim-style navigation | 10 | ✅ Active |
-| **dashboard-client** | `core/crates/client/` | Leptos WASM CSR dashboard (modern, recommended) | - | ✅ Active |
-| **dashboard-shared** | `core/crates/dashboard-shared` | Shared types for dashboard | 4 | ✅ Active |
-| **syntaxis-api** | `core/crates/syntaxis-api` | REST API server via axum, serves dashboard | - | ✅ Active |
-| **syntaxis-dashboard** | `core/crates/wrks/dashboard` | DEPRECATED: Old web dashboard (legacy server) | 52 | ⚠️ Deprecated |
-| **syntaxis-vapora** | `core/crates/syntaxis-vapora` | VAPORA orchestration adapter | 57 | ✅ Active |
-
-### Shared Libraries
-
-| Component | Location | Tests | Status |
-|-----------|----------|-------|--------|
-| **shared-api-lib** | `shared/rust-api/shared-api-lib` | REST API utilities | 93 | ✅ Active |
-| **rust-tui** | `shared/rust-tui` | TUI utilities (ratatui helpers) | 262 | ✅ Active |
-| **tools-shared** | `shared/rust` | Configuration, utilities, helpers | 33 | ✅ Active |
-
-### Workspace Structure
-```
-syntaxis/ (MONOREPO ROOT)
-├── shared/                    # Reusable libraries
-│   ├── rust-api/             # REST API library
-│   ├── rust-tui/             # TUI utilities
-│   └── rust/                 # Config, utilities
-├── syntaxis/         # Main project (6+ crates)
-│   ├── crates/               # Individual crates
-│   ├── docs/                 # Architecture docs
-│   ├── scripts/              # NuShell build scripts
-│   └── Cargo.toml
-├── .coder/                    # Project tracking (NEVER REMOVE)
-├── .claude/                   # Development guidelines
-├── Justfile                  # Build recipes
-├── Cargo.toml               # Root workspace
-└── README.md
-```
-
-## Key Architectural Patterns
-
-### Module Organization (syntaxis-core example)
-```rust
-mod error;              // Error types (thiserror)
-mod types;              // Domain types (Project, Task, Phase)
-mod config;             // Configuration (TOML + Serde)
-mod persistence;        // Database layer (SQLite + sqlx)
-mod phase;              // Phase management
-mod phase_actions;      // Phase state transitions
-mod phase_enhanced;      // Extended phase logic
-mod audit;              // Change tracking & audit trail
-mod checklist;          // Phase-based checklists
-mod templates;          // Project templates
-mod tools;              // Tool management
-mod security;           // Security utilities
-#[cfg(test)] mod tests { ... }  // Comprehensive tests
-```
-
-### Error Handling Pattern
-All modules use `thiserror` for custom error types with `Result<T>` returns:
-```rust
-use thiserror::Error;
-
-#[derive(Error, Debug)]
-pub enum WorkspaceError {
-    #[error("IO error: {0}")]
-    Io(#[from] std::io::Error),
-    #[error("Database error: {0}")]
-    Database(String),
-}
-
-pub type Result<T> = std::result::Result<T, WorkspaceError>;
-```
-
-### Configuration-Driven Design
-- All settings via TOML + Serde (no hardcoded values)
-- `find-config` NuShell utility discovers config files in order:
-  1. `.syntaxis/{filename}`
-  2. `.project/{filename}`
-  3. `.coder/{filename}`
-  4. Current directory
-
-### Database Layer (SurrealDB 2.3 + SQLite Support)
-- **SurrealDB 2.3**: Modern multi-backend database (embedded & server modes)
-  - Supports embedded in-memory, file-based (RocksDB), and server modes
-  - Feature-gated optional dependency: enable with `surrealdb` feature
-  - Type-safe async operations with `Database` trait abstraction
-  - 40+ database operations fully implemented
-  - Configuration: `configs/database-surrealdb.toml`
-- **SQLite (Default)**: File-based relational database
-  - Async runtime (tokio + sqlx) with Connection pooling
-  - Prepared statements for security & performance
-  - Configuration: `configs/database-default.toml`
-- **Trait-Based Design**: Single `Database` trait enables multiple implementations
-  - `SqliteDatabase` for SQLite backend
-  - `SurrealDatabase` for SurrealDB backend
-  - Runtime selection via configuration file
-- Located in `syntaxis-core/src/persistence/` module with surrealdb_impl.rs
-
-### Multi-Interface Design
-- **CLI**: Command-line via clap with structured arguments
-- **TUI**: Terminal UI via ratatui with vim-style keybindings (hjkl)
-- **Dashboard**: Web UI via Leptos (CSR WASM client)
-- **API**: REST endpoints via axum with Tower middleware
-
-## Code Quality Standards
-
-### Mandatory Requirements
-✅ **No unsafe code** - `#![forbid(unsafe_code)]` enforced
-✅ **No unwrap()** - Use `Result<T>` with `?` operator
-✅ **100% documented** - All public APIs have rustdoc
-✅ **691+ tests** - Minimum 15 tests per module (all passing)
-✅ **Formatted** - Passes `cargo fmt --all`
-✅ **Linted** - Passes `cargo clippy --all-targets` (zero warnings)
-✅ **Audited** - Passes `cargo audit`
-✅ **SurrealDB 2.3** - Production-ready multi-backend database support
-
-### Pre-Commit Checklist
-- [ ] `cargo fmt --all` (code formatted)
-- [ ] `cargo clippy --all-targets` (zero warnings)
-- [ ] `cargo test --workspace` (all 691+ tests pass)
-- [ ] `cargo audit` (no vulnerabilities)
-- [ ] Rustdoc for all public items
-- [ ] No unsafe code
-- [ ] No unwrap() in production code
-- [ ] SurrealDB configuration tested (if using)
-
-## Important Guidelines
-
-### Never
-- Remove `.coder` directory (contains project lifecycle tracking)
-- Use `unsafe` code
-- Use `unwrap()` in production code
-- Hardcode configuration values
-- Simplify code when bugs are found
-
-### Always
-- Format, lint, test, and document code
-- **Fix bugs completely** - don't simplify code when issues arise
-- Use proper error handling with `Result<T>`
-- Document public APIs with rustdoc
-- Write tests first (TDD approach)
-- Use idiomatic Rust patterns
-
-## Development Workflow
-
-### For Bug Fixes
-1. Locate the bug using provided error context
-2. Write failing test demonstrating the issue
-3. Fix the bug completely (don't simplify)
-4. Ensure all 632+ tests pass
-5. Verify lint, format, and audit pass
-
-### For New Features
-1. Plan module structure following existing patterns
-2. Write tests first (TDD)
-3. Implement feature with proper error handling
-4. Document public APIs with rustdoc
-5. Run full verification: `just check-all`
-
-### For Refactoring
-1. Keep all tests passing during refactoring
-2. Extract common patterns into utilities
-3. Use configuration for flexibility
-4. Maintain backwards compatibility where possible
-5. Update documentation
-
-## Infrastructure & Scripts
-
-NuShell scripts in `scripts/` handle infrastructure:
-
-- `install-cli.nu` - Auto-discover and install binaries
-- `manifest.nu` - Track installed binaries
-- `common/find-config.nu` - Configuration discovery utility
-
-Example: `nu scripts/install-cli.nu all` installs all workspace binaries.
-
-## VAPORA Integration
-
-syntaxis is designed as the foundation for VAPORA SST (Software Specification & Tasks):
-
-**Key concepts for VAPORA integration**:
-- **Project**: Top-level container (id, name, metadata)
-- **Phase**: Project lifecycle stages (create, devel, publish, archive)
-- **Task**: Work items with state tracking and audit trail
-- **Audit**: Full change history enabling state rollback
-
-**VAPORA uses syntaxis for**:
-- Project and task definitions
-- Task state tracking
-- Phase-based orchestration
-- Agent triggering based on pending tasks
-- Enterprise-grade change tracking
-
-## SurrealDB 2.3 Integration
-
-**syntaxis now fully supports SurrealDB 2.3** as an alternative database backend.
-
-### Deployment Options
-
-| Mode | Best For | Configuration |
-|------|----------|---------------|
-| **In-Memory** | Development, unit tests, CI/CD | `url = "mem://"` |
-| **File-Based** | Local development with persistence | `url = "file:///path/to/db"` |
-| **Server Mode** | Integration testing, multiple clients | `surreal start --bind 127.0.0.1:8000 memory` |
-| **Docker** | Development teams, reproducible setup | `docker-compose.surrealdb.yml` |
-| **Kubernetes** | Production, enterprise deployment | `k8s/` manifests |
-
-### Quick Start
-
-**Switch to SurrealDB**:
-```bash
-cp configs/database-surrealdb.toml configs/database.toml
-surreal start --bind 127.0.0.1:8000 memory
-cargo run -p syntaxis-cli
-```
-
-**Switch back to SQLite**:
-```bash
-cp configs/database-default.toml configs/database.toml
-cargo run -p syntaxis-cli
-```
-
-### SurrealDB Implementation Details
-
-- **Location**: `syntaxis-core/src/persistence/surrealdb_impl.rs` (800+ lines)
-- **Operations**: 40+ database methods fully implemented
-- **Feature**: Optional, enabled by default via `surrealdb` Cargo feature
-- **API**: Modern JSON binding pattern with `bind(json!({"key": value}))`
-- **Tests**: 4 implementations (1 passing, 3 ignored for embedded mode sync)
-- **Integration Tests**: 16 server-mode tests in `tests/integration_surrealdb.rs`
-
-### Configuration Files
-
-- **`configs/database-default.toml`**: SQLite configuration (recommended default)
-- **`configs/database-surrealdb.toml`**: SurrealDB configuration with all options documented
-- **Environment Variables**: Support for `SURREALDB_PASSWORD` and other secrets
-
-### Documentation
-
-- **SURREALDB_QUICK_START.md**: Get started in 5 minutes
-- **SURREALDB_SETUP_GUIDE.md**: Complete setup for local, Docker, Kubernetes
-- **SURREALDB_2_3_MIGRATION.md**: Detailed migration information and API changes
-- **DEPENDENCIES.md**: SurrealDB 2.3 in Tier 1 (critical dependencies)
-
-### Key Architecture Decisions
-
-1. **Trait-Based Abstraction**: Single `Database` trait with multiple implementations
-2. **Runtime Selection**: Database backend chosen via configuration, not compile-time
-3. **Feature-Gated**: SurrealDB is optional - can build without it if needed
-4. **Type Safety**: All operations use Rust's type system for compile-time safety
-5. **Async Throughout**: All database operations are async with tokio runtime
-
-## Performance Considerations
-
-### Database Performance
-
-**SurrealDB 2.3**:
-- Connection pooling for efficient resource use
-- Type-safe queries prevent SQL injection
-- Embedded mode offers near-memory speeds
-- Server mode supports clustering for scalability
-
-**SQLite**:
-- Connection pooling via SQLitePool
-- Batch operations for multiple updates
-- Indexed queries for common lookups
-- SQLite pragmas for WAL mode and cache
-
-### API Performance
-- Tower middleware for compression
-- Rate limiting and request/response caching
-- Async/await throughout (tokio runtime)
-- Minimal allocations in hot paths
-
-### TUI Performance
-- Efficient terminal drawing via ratatui
-- Minimal redraws (only changed regions)
-- Async task loading with progress indicators
-
-## Related Documentation
-
-- **README.md** - Project overview and quick start
-- **.claude/PROJECT_RULES.md** - Architecture principles and standards
-- **.claude/CODE_STANDARDS.md** - Build, test, and verification guidelines
-- **.claude/DEVELOPMENT.md** - Development workflow and patterns
-- **core/docs/ARCHITECTURE.md** - Detailed system design
-- **scripts/README.md** - Infrastructure scripts documentation
-
-## Current Status
-
-- ✅ **Phase 1-12**: Core functionality complete (173+ tests in syntaxis-core)
-- ✅ **Multi-interface**: CLI, TUI, Dashboard all operational
-- ⚠️ **syntaxis-api**: REST API in progress (37 compilation errors)
-- 🔜 **syntaxis-vapora**: VAPORA adapter planned
-- ✅ **Tests**: 632+ tests passing across 8 crates
-- ✅ **Production-ready**: Beta status, final integration pending
-
-## Quick Troubleshooting
-
-```bash
-# Compilation clean rebuild
-cargo clean && cargo check --workspace
-
-# Test failures with logging
-RUST_LOG=debug cargo test -- --nocapture
-
-# Serial test execution (single-threaded)
-cargo test -- --test-threads=1
-
-# Reset SQLite databases
-rm -f data/*.db && cargo test --workspace
-
-# Performance profiling
-cargo flamegraph
-cargo bench
-```
-
----
-
-**Last Updated**: 2025-11-15
-**Rust Edition**: 2021 (MSRV 1.75+)
-**Total Tests**: 632+ passing
-**Lines of Code**: 10K+ (syntaxis-core alone)