Add an example app with paths extraction

.github/workflows/ci-publishing-jar-files.yaml

@@ -0,0 +1,26 @@
+name: Publish package to GitHub Packages
+on:
+  release:
+    types: [created]
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+      - name: Setup JDK 21
+        uses: actions/setup-java@v5
+        with:
+          distribution: 'temurin'
+          java-version: '21'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v6
+      - name: Run tests
+        run: ./gradlew test
+      - name: Publish package
+        run: ./gradlew publish --stacktrace
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci-test-infrastructure.yaml

@@ -0,0 +1,35 @@
+name: Run tests and test coverage
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+permissions:
+  pull-requests: write
+  contents: read
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+      - name: Set up JDK 21
+        uses: actions/setup-java@v5
+        with:
+          distribution: 'temurin'
+          java-version: '21'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v6
+      - name: Run tests and verify coverage
+        run: ./gradlew --no-daemon testCodeCoverageReport
+
+      - name: Add coverage to PR
+        id: jacoco
+        uses: madrapps/jacoco-report@v1.8.0
+        with:
+          paths: ${{ github.workspace }}/build/reports/jacoco/testCodeCoverageReport/testCodeCoverageReport.xml
+          token: ${{ secrets.GITHUB_TOKEN }}
+          min-coverage-overall: 95
+          min-coverage-changed-lines: 0
+
+      - name: Verify coverage
+        run: ./gradlew jacocoTestCoverageVerification

.gitignore

@@ -1,7 +1,12 @@
+# Tests output
+./test-shared/gen/
+
 # Log file
 *.log
 *.logs
 
+bin/
+
 .gradle
 !gradle/wrapper/gradle-wrapper.jar
 **/build/
@@ -28,4 +33,4 @@
 !/benchmarks/src/main/java/org/ucfs/scanner/*.flex
 
 ### Large datasets ###
-/benchmarks/src/test/resources/java/correct/*
+/benchmarks/src/test/resources/java/correct/*

AGENTS.md

@@ -0,0 +1,148 @@
+# AGENTS.md
+
+This file helps AI agents understand and work with the UCFS codebase.
+
+## Project Overview
+
+**UCFS** (Universal Context-Free Solver) is a Kotlin library that performs context-free path querying on edge-labeled directed graphs using a modified GLL (Generalized LL) parsing algorithm with Recursive State Machines (RSM).
+
+**Key capabilities:**
+- Parse arbitrary directed graphs against context-free grammars
+- Produce SPPF (Shared Packed Parse Forest) — compact representation of all matching paths
+- Support for grammar definition via Kotlin DSL
+- DOT graph format support
+
+## Module Structure
+
+| Module | Description |
+|--------|-------------|
+| `solver/` | Core library — GLL parser, RSM, grammar DSL, SPPF, input graph |
+| `generator/` | Code generator built on solver — AST extraction, parser generation |
+| `test-shared/` | Shared test infrastructure, dynamic tests, ANTLR4 comparison |
+| `cfpq-paths-app/` | Runnable demo application with examples |
+
+### Module Dependencies
+
+```mermaid
+graph TD
+    Solver[solver]
+    Generator[generator] --> Solver
+    TestShared[test-shared] --> Solver
+    TestShared --> Generator
+    App[cfpq-paths-app] --> Solver
+```
+
+## Build System
+
+- **Tool:** Gradle with Kotlin DSL (`build.gradle.kts`)
+- **Wrapper:** `./gradlew` included, no local Gradle install needed
+- **JDK:** 21+ (toolchain configured in each module)
+- **Kotlin:** 2.4.0
+
+### Essential Commands
+
+```bash
+./gradlew build                        # Build all modules
+./gradlew test                         # Run all tests
+./gradlew testCodeCoverageReport       # Generate coverage report (HTML + XML)
+./gradlew jacocoTestCoverageVerification  # Verify coverage thresholds
+./gradlew :cfpq-paths-app:runSimpleExamples  # Run demo examples
+```
+
+### Coverage Thresholds
+
+| Counter | Minimum |
+|---------|---------|
+| Instruction | 95% |
+| Branch | 80% |
+| Line | 80% |
+| Method | 85% |
+| Class | 90% |
+
+## Code Conventions
+
+- **Style:** `kotlin.code.style=official` (set in `gradle.properties`)
+- **Package root:** `org.ucfs` for all modules
+- **Naming:** PascalCase for classes, camelCase for functions/properties
+- **Testing:** JUnit 5 with `useJUnitPlatform()`
+
+## Documentation Conventions
+
+- **Structured over ASCII:** Use Mermaid diagrams (`graph TD`, `flowchart LR`) and tables instead of ASCII art or text-based schemas — they render natively on GitHub
+- **Unified style:** All documentation follows a consistent structure: purpose → prerequisites → content → cross-references
+- **Developer docs:** Place in `dev/` directory; user-facing docs go to `docs/docs/`
+
+## Agent Workflow Rules
+
+### General Workflow
+
+1. **Plan-first policy:** Before making any changes, present a plan of what will be changed and why. Wait for user approval before executing.
+2. **No commits without explicit request:** Never `git commit` or `git push` unless the user explicitly asks. Present diffs for review first.
+3. **Verify before presenting:** Build and tests must pass before showing changes as ready for review.
+4. **Conventional commits:** All commit messages must follow the format from [CONTRIBUTING.md](CONTRIBUTING.md):
+   - Format: `type(scope): short description`
+   - Types: `feat`, `fix`, `docs`, `style`, `refactor`, `test`, `chore`
+   - Example: `chore(build): update JDK toolchain from 11 to 21`
+
+### Documentation-First Policy
+
+> Any structural or behavioral change must be reflected in the agent documentation *before* implementation.
+
+1. Update relevant files in `dev/` (and `AGENTS.md`) to reflect the intended change
+2. **Ask the user to approve the documentation changes**
+3. Only after approval, commit the documentation changes
+4. Then implement the actual code changes
+
+### Documentation update rules
+
+When refactoring public API (e.g., renaming DSL functions), update **all** documentation:
+
+1. **Search scope:** Always search the **entire repository**, not just `docs/docs/`. Include `README.md`, `dev/*.md`, and `docs/docs/*.md` in every grep.
+2. **Verify against source:** After updating docs, cross-check each code snippet against the actual API signature in source code (e.g., confirm `asStart()` takes no arguments by reading `Grammar.kt`).
+3. **Build verification:** Run `./gradlew build` after any change that touches documented API to catch stale examples that no longer compile.
+
+## Key Source Files
+
+| File | Purpose |
+|------|---------|
+| `solver/.../parser/Gll.kt` | Main GLL parser implementation |
+| `solver/.../grammar/combinator/Grammar.kt` | Grammar DSL base class |
+| `solver/.../rsm/RsmState.kt` | RSM state representation |
+| `solver/.../gss/GraphStructuredStack.kt` | GSS data structure for GLL |
+| `solver/.../sppf/SppfStorage.kt` | SPPF node management |
+| `solver/.../input/InputGraph.kt` | Input graph representation |
+| `generator/.../ast/AstExtractor.kt` | AST extraction from SPPF |
+
+## Key Abstractions
+
+- **`Grammar`** — DSL base class; users extend it to define CFGs
+- **`RsmState`** — Recursive State Machine state; grammar compiles to RSM
+- **`Gll`** — Parser that runs RSM against input graph
+- **`IInputGraph<V, L>`** — Generic graph interface with vertices and labeled edges
+- **`RangeSppfNode`** — SPPF node representing a range of matched input
+- **`Descriptor<V>`** — Processing unit in GLL: (position, GSS node, RSM state, SPPF node)
+
+## Data Flow
+
+```mermaid
+flowchart LR
+    Grammar[User Grammar DSL] --> RSM[RSM]
+    RSM --> GLL[Gll.parse]
+    GLL --> SPPF[SPPF]
+    SPPF --> Results[Path extraction / AST]
+    Graph[Input Graph DOT/code] --> GLL
+```
+
+## CI/CD
+
+Three GitHub Actions workflows:
+- `ci-test-infrastructure.yaml` — Tests + JaCoCo coverage on push/PR
+- `ci-docs.yaml` — MkDocs site deployment
+- `ci-publishing-jar-files.yaml` — Maven package publishing to GitHub Packages
+
+## Documentation
+
+- **User docs:** `docs/docs/` (MkDocs, deployed to GitHub Pages)
+- **Developer docs:** `dev/` directory
+  - `dev/ARCHITECTURE.md` — Detailed architecture overview
+  - `dev/DEVELOPMENT.md` — Local development setup guide

CHANGELOG.md

@@ -0,0 +1,21 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- Developer documentation in `dev/` directory
+- `AGENTS.md` for AI-assisted development
+- `ARCHITECTURE.md` with module and data flow overview
+- `DEVELOPMENT.md` with local setup guide
+- `CONTRIBUTING.md` with contribution guidelines
+- `CODE_OF_CONDUCT.md`
+
+### Changed
+
+- Enhanced `README.md` with badges and improved structure

CODE_OF_CONDUCT.md

@@ -0,0 +1,62 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at the project
+maintainers. All complaints will be reviewed and investigated promptly and
+fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org),
+version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.