Fix critical bugs and simplify CLI interface

.github/CODECOV_SETUP.md

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+# Codecov Setup Guide
+
+To enable code coverage reporting with Codecov, follow these steps:
+
+## 1. Sign up for Codecov
+
+1. Go to [codecov.io](https://codecov.io)
+2. Sign in with your GitHub account
+3. Authorize Codecov to access your repositories
+
+## 2. Add Repository
+
+1. Find `Kydoimos97/FileCombiner` in your repository list
+2. Click "Setup repo" or enable it
+
+## 3. Get Upload Token
+
+1. Go to repository settings in Codecov
+2. Copy the upload token (it will look like: `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx`)
+
+## 4. Add Token to GitHub Secrets
+
+1. Go to your GitHub repository: `https://github.com/Kydoimos97/FileCombiner`
+2. Click on **Settings** → **Secrets and variables** → **Actions**
+3. Click **New repository secret**
+4. Name: `CODECOV_TOKEN`
+5. Value: Paste the token from Codecov
+6. Click **Add secret**
+
+## 5. Verify Setup
+
+Once the token is added:
+1. Push a commit or create a PR
+2. The CI workflow will run automatically
+3. Coverage reports will be uploaded to Codecov
+4. The coverage badge in README.md will update
+
+## Optional: Configure Codecov
+
+Create a `codecov.yml` file in the repository root to customize coverage settings:
+
+```yaml
+coverage:
+  status:
+    project:
+      default:
+        target: 80%
+        threshold: 1%
+    patch:
+      default:
+        target: 80%
+
+comment:
+  layout: "reach,diff,flags,tree"
+  behavior: default
+  require_changes: false
+```
+
+## Troubleshooting
+
+- **Badge shows "unknown"**: Token not set or first workflow hasn't completed yet
+- **Coverage not uploading**: Check GitHub Actions logs for errors
+- **Token invalid**: Regenerate token in Codecov and update GitHub secret
+
+## Resources
+
+- [Codecov Documentation](https://docs.codecov.com/)
+- [GitHub Actions Integration](https://docs.codecov.com/docs/github-actions-integration)

.github/CODECOV_STATUS.md

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+# Codecov Integration Status
+
+## ✅ Completed Setup
+
+1. **GitHub Actions CI Workflow** (`.github/workflows/ci.yml`)
+   - Runs tests on Ubuntu, Windows, and macOS
+   - Collects code coverage using XPlat Code Coverage (coverlet)
+   - Uploads coverage to Codecov using v5 action
+   - Builds Windows x64 artifacts on main branch
+
+2. **Codecov Configuration** (`codecov.yml`)
+   - Target coverage: 70%
+   - Ignores test files and build artifacts
+   - Configured for PR comments with coverage diff
+
+3. **README Badges**
+   - CI status badge
+   - Codecov coverage badge
+   - License and .NET version badges
+
+4. **Test Project Configuration**
+   - `coverlet.collector` package installed (v6.0.2)
+   - Configured to generate Cobertura XML format
+
+## 🔧 Required: User Action
+
+**You need to add the CODECOV_TOKEN to GitHub Secrets:**
+
+1. Go to [Codecov.io](https://codecov.io) and sign in with GitHub
+2. Find your repository: `Kydoimos97/FileCombiner`
+3. Copy the upload token from repository settings
+4. Go to GitHub: `https://github.com/Kydoimos97/FileCombiner/settings/secrets/actions`
+5. Click "New repository secret"
+6. Name: `CODECOV_TOKEN`
+7. Value: Paste your token
+8. Save
+
+## 📊 Current Status
+
+- Latest commit: `96ebbc0` - "fix: update codecov action to v5 and simplify coverage upload"
+- Branch: `feature/cli-fixes-and-simplification`
+- Status: **Pushed and ready for CI run**
+
+## 🔍 What Happens Next
+
+Once you add the `CODECOV_TOKEN`:
+
+1. The CI workflow will run on the next push/PR
+2. Tests will execute on all three platforms
+3. Coverage will be collected from Ubuntu runner
+4. Coverage report will upload to Codecov
+5. Badges in README will update with real data
+
+## 🐛 Troubleshooting
+
+If coverage upload fails:
+
+1. **Check token is set**: Verify `CODECOV_TOKEN` exists in GitHub Secrets
+2. **Check workflow logs**: Look for "Upload coverage reports to Codecov" step
+3. **Verify coverage files**: The workflow expects `./coverage/**/coverage.cobertura.xml`
+4. **Check Codecov dashboard**: Visit codecov.io to see upload status
+
+## 📝 Files Modified
+
+- `.github/workflows/ci.yml` - CI workflow with Codecov integration
+- `codecov.yml` - Codecov configuration
+- `README.md` - Added badges
+- `.github/CODECOV_SETUP.md` - Setup instructions (reference)
+
+## ✨ Next Steps
+
+1. Add `CODECOV_TOKEN` to GitHub Secrets (required)
+2. Merge PR #1 to main branch
+3. Verify CI passes and coverage uploads
+4. Check coverage badge updates in README
+
+---
+
+**Note**: The workflow uses `fail_ci_if_error: false` so CI won't fail if Codecov upload has issues. This is intentional during initial setup. You can change it to `true` once everything is working.

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, develop, feature/* ]
+  pull_request:
+    branches: [ main, develop ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: '8.0.x'
+
+    - name: Restore dependencies
+      run: dotnet restore
+
+    - name: Build
+      run: dotnet build --configuration Release --no-restore
+
+    - name: Run tests with coverage
+      run: dotnet test FileCombiner.Tests/FileCombiner.Tests.csproj /p:CollectCoverage=true /p:CoverletOutputFormat=cobertura /p:CoverletOutput=../coverage.cobertura.xml --configuration Release --verbosity quiet
+
+    - name: List coverage files (debug)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        echo "Searching for coverage files..."
+        ls -la *.xml || echo "No XML files found"
+        echo "=== Coverage file content (first 50 lines) ==="
+        head -50 coverage.cobertura.xml || echo "Cannot read coverage.cobertura.xml"
+        echo "=== Coverage file stats ==="
+        grep -E 'line-rate|branch-rate|lines-covered|lines-valid' coverage.cobertura.xml | head -5 || echo "Cannot parse coverage stats"
+
+    - name: Upload coverage reports to Codecov
+      if: matrix.os == 'ubuntu-latest'
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.cobertura.xml
+        flags: unittests
+        fail_ci_if_error: false
+        verbose: true
+
+  build:
+    name: Build Release Artifacts
+    runs-on: windows-latest
+    needs: test
+    if: github.ref == 'refs/heads/main'
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: '8.0.x'
+
+    - name: Publish Windows x64
+      run: dotnet publish -c Release -r win-x64 --self-contained true -p:PublishSingleFile=true -p:DebugType=None -p:DebugSymbols=false -o ./artifacts/win-x64
+
+    - name: Upload Windows artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: filecombiner-win-x64
+        path: ./artifacts/win-x64/filecombiner.exe
+        retention-days: 30

.gitignore

@@ -2,3 +2,77 @@
 /bin/
 /obj/
 /*.DotSettings.user
+
+# Kiro IDE files
+.kiro/
+
+# Coverage reports
+coverage*.xml
+coveragereport/
+TestResults/
+
+# Build results
+[Dd]ebug/
+[Dd]ebugPublic/
+[Rr]elease/
+[Rr]eleases/
+x64/
+x86/
+[Ww][Ii][Nn]32/
+[Aa][Rr][Mm]/
+[Aa][Rr][Mm]64/
+bld/
+[Bb]in/
+[Oo]bj/
+[Ll]og/
+[Ll]ogs/
+
+# Test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+# Files built by Visual Studio
+*_i.c
+*_p.c
+*_h.h
+*.ilk
+*.meta
+*.obj
+*.iobj
+*.pch
+*.pdb
+*.ipdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*_wpftmp.csproj
+*.log
+*.tlog
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.svclog
+*.scc
+
+# Visual Studio cache/options
+.vs/
+.vscode/
+
+# ReSharper
+_ReSharper*/
+*.[Rr]e[Ss]harper
+*.DotSettings.user
+
+# User-specific files
+*.rsuser
+*.suo
+*.user
+*.userosscache
+*.sln.docstates

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "kiroAgent.configureMCP": "Disabled"
+}

CHANGELOG.md

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+# Changelog
+
+All notable changes to FileCombiner will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- `--interactive` / `-i` flag for opt-in interactive mode
+- Comprehensive property-based testing with FsCheck
+- Improved help text using CommandLine library's built-in help generation
+- Path resolution tests to ensure location independence
+
+### Changed
+- **BREAKING**: Interactive mode is now opt-in via `--interactive` flag instead of automatic fallback
+- **BREAKING**: Directory argument is now optional (defaults to current directory)
+- Simplified interactive mode from 7 questions to 4 essential questions
+- Help text now uses CommandLine library's automatic generation
+- Fixed Spectre.Console markup escaping in help display
+- Fixed service initialization hang caused by circular dependency
+- Improved async/await patterns throughout codebase
+
+### Removed
+- **BREAKING**: The following options are now hidden (still work for backward compatibility):
+  - `--include` - Use `--extensions` instead
+  - `--ignore-dirs` - Use `--exclude` with directory patterns instead
+  - `--compact` - Feature removed (rarely used)
+  - `--no-tree` - Tree generation simplified
+  - `--max-files` - Now uses sensible default of 1000
+  - `--max-file-size` - Now uses sensible default of 10MB
+
+### Fixed
+- Spectre.Console markup parsing errors in help display
+- Application hanging after service provider initialization
+- Circular dependency between ContentExtractorFactory and FileContentExtractor
+
+## Migration Guide
+
+### For users of removed options:
+
+**`--include` patterns**
+- **Before**: `filecombiner . --include "*.cs,*.js"`
+- **After**: `filecombiner . --extensions .cs,.js`
+
+**`--ignore-dirs` patterns**
+- **Before**: `filecombiner . --ignore-dirs "bin,obj"`
+- **After**: `filecombiner . --exclude "**/bin/**,**/obj/**"`
+
+**`--compact` mode**
+- This feature has been removed. The default output format is now optimized.
+
+**`--no-tree` flag**
+- Tree generation is now always included and optimized.
+
+**`--max-files` and `--max-file-size`**
+- These now use sensible defaults (1000 files, 10MB per file).
+- If you need different limits, please open an issue.
+
+### For users relying on automatic interactive mode:
+
+**Before**: Running `filecombiner` without arguments would enter interactive mode.
+
+**After**: Running `filecombiner` without arguments processes the current directory with defaults.
+
+To enter interactive mode, use the `--interactive` or `-i` flag:
+```bash
+filecombiner --interactive
+```
+
+### Default behavior changes:
+
+- **No arguments**: Now processes current directory instead of entering interactive mode
+- **Directory only**: `filecombiner ./src` now works without additional prompts
+- **Sensible defaults**: Auto-detects text files, max depth of 5, outputs to clipboard
+
+## [Previous Versions]
+
+_(No previous versions documented)_