chore: modernize workflows, security scanning, and linting configuration (#50)

* build: update Go 1.25, CI workflows, and build tooling

- Upgrade to Go 1.25
- Add benchmark targets to Makefile
- Implement parallel gosec execution
- Lock tool versions for reproducibility
- Add shellcheck directives to scripts
- Update CI workflows with improved caching

* refactor: migrate from golangci-lint to revive

- Replace golangci-lint with revive for linting
- Configure comprehensive revive rules
- Fix all EditorConfig violations
- Add yamllint and yamlfmt support
- Remove deprecated .golangci.yml

* refactor: rename utils to shared and deduplicate code

- Rename utils package to shared
- Add shared constants package
- Deduplicate constants across packages
- Address CodeRabbit review feedback

* fix: resolve SonarQube issues and add safety guards

- Fix all 73 SonarQube OPEN issues
- Add nil guards for resourceMonitor, backpressure, metricsCollector
- Implement io.Closer for headerFileReader
- Propagate errors from processing helpers
- Add metrics and templates packages
- Improve error handling across codebase

* test: improve test infrastructure and coverage

- Add benchmarks for cli, fileproc, metrics
- Improve test coverage for cli, fileproc, config
- Refactor tests with helper functions
- Add shared test constants
- Fix test function naming conventions
- Reduce cognitive complexity in benchmark tests

* docs: update documentation and configuration examples

- Update CLAUDE.md with current project state
- Refresh README with new features
- Add usage and configuration examples
- Add SonarQube project configuration
- Consolidate config.example.yaml

* fix: resolve shellcheck warnings in scripts

- Use ./*.go instead of *.go to prevent dash-prefixed filenames
  from being interpreted as options (SC2035)
- Remove unreachable return statement after exit (SC2317)
- Remove obsolete gibidiutils/ directory reference

* chore(deps): upgrade go dependencies

* chore(lint): megalinter fixes

* fix: improve test coverage and fix file descriptor leaks

- Add defer r.Close() to fix pipe file descriptor leaks in benchmark tests
- Refactor TestProcessorConfigureFileTypes with helper functions and assertions
- Refactor TestProcessorLogFinalStats with output capture and keyword verification
- Use shared constants instead of literal strings (TestFilePNG, FormatMarkdown, etc.)
- Reduce cognitive complexity by extracting helper functions

* fix: align test comments with function names

Remove underscores from test comments to match actual function names:
- benchmark/benchmark_test.go (2 fixes)
- fileproc/filetypes_config_test.go (4 fixes)
- fileproc/filetypes_registry_test.go (6 fixes)
- fileproc/processor_test.go (6 fixes)
- fileproc/resource_monitor_types_test.go (4 fixes)
- fileproc/writer_test.go (3 fixes)

* fix: various test improvements and bug fixes

- Remove duplicate maxCacheSize check in filetypes_registry_test.go
- Shorten long comment in processor_test.go to stay under 120 chars
- Remove flaky time.Sleep in collector_test.go, use >= 0 assertion
- Close pipe reader in benchmark_test.go to fix file descriptor leak
- Use ContinueOnError in flags_test.go to match ResetFlags behavior
- Add nil check for p.ui in processor_workers.go before UpdateProgress
- Fix resource_monitor_validation_test.go by setting hardMemoryLimitBytes directly

* chore(yaml): add missing document start markers

Add --- document start to YAML files to satisfy yamllint:
- .github/workflows/codeql.yml
- .github/workflows/build-test-publish.yml
- .github/workflows/security.yml
- .github/actions/setup/action.yml

* fix: guard nil resourceMonitor and fix test deadlock

- Guard resourceMonitor before CreateFileProcessingContext call
- Add ui.UpdateProgress on emergency stop and path error returns
- Fix potential deadlock in TestProcessFile using wg.Go with defer close

fileproc/collector_test.go

@@ -2,6 +2,7 @@ package fileproc_test
 
 import (
 	"os"
+	"path/filepath"
 	"testing"
 
 	"github.com/ivuorinen/gibidify/fileproc"
@@ -47,3 +48,70 @@ func TestCollectFilesError(t *testing.T) {
 		t.Fatal("Expected an error, got nil")
 	}
 }
+
+// TestCollectFiles tests the actual CollectFiles function with a real directory.
+func TestCollectFiles(t *testing.T) {
+	// Create a temporary directory with test files
+	tmpDir := t.TempDir()
+
+	// Create test files with known supported extensions
+	testFiles := map[string]string{
+		"test1.go": "package main\n\nfunc main() {\n\t// Go file\n}",
+		"test2.py": "# Python file\nprint('hello world')",
+		"test3.js": "// JavaScript file\nconsole.log('hello');",
+	}
+
+	for name, content := range testFiles {
+		filePath := filepath.Join(tmpDir, name)
+		if err := os.WriteFile(filePath, []byte(content), 0o600); err != nil {
+			t.Fatalf("Failed to create test file %s: %v", name, err)
+		}
+	}
+
+	// Test CollectFiles
+	files, err := fileproc.CollectFiles(tmpDir)
+	if err != nil {
+		t.Fatalf("CollectFiles failed: %v", err)
+	}
+
+	// Verify we got the expected number of files
+	if len(files) != len(testFiles) {
+		t.Errorf("Expected %d files, got %d", len(testFiles), len(files))
+	}
+
+	// Verify all expected files are found
+	foundFiles := make(map[string]bool)
+	for _, file := range files {
+		foundFiles[file] = true
+	}
+
+	for expectedFile := range testFiles {
+		expectedPath := filepath.Join(tmpDir, expectedFile)
+		if !foundFiles[expectedPath] {
+			t.Errorf("Expected file %s not found in results", expectedPath)
+		}
+	}
+}
+
+// TestCollectFiles_NonExistentDirectory tests CollectFiles with a non-existent directory.
+func TestCollectFilesNonExistentDirectory(t *testing.T) {
+	_, err := fileproc.CollectFiles("/non/existent/directory")
+	if err == nil {
+		t.Error("Expected error for non-existent directory, got nil")
+	}
+}
+
+// TestCollectFiles_EmptyDirectory tests CollectFiles with an empty directory.
+func TestCollectFilesEmptyDirectory(t *testing.T) {
+	tmpDir := t.TempDir()
+	// Don't create any files
+
+	files, err := fileproc.CollectFiles(tmpDir)
+	if err != nil {
+		t.Fatalf("CollectFiles failed on empty directory: %v", err)
+	}
+
+	if len(files) != 0 {
+		t.Errorf("Expected 0 files in empty directory, got %d", len(files))
+	}
+}