Internalize majority of cmd package (#2533)

* internalize majority of cmd package and migrate integration tests

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

* add internal api encoder

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

* create internal representation of all formats

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

* export capability to get default encoders

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

* restore test fixtures

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

---------

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

cmd/syft/internal/test/integration/regression_java_virtualpath_test.go

@@ -0,0 +1,36 @@
+package integration
+
+import (
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/source"
+)
+
+func TestWarCatalogedCorrectlyIfRenamed(t *testing.T) {
+	// install hudson-war@2.2.1 and renames the file to `/hudson.war`
+	sbom, _ := catalogFixtureImage(t, "image-java-virtualpath-regression", source.SquashedScope)
+
+	badPURL := "pkg:maven/hudson/hudson@2.2.1"
+	goodPURL := "pkg:maven/org.jvnet.hudson.main/hudson-war@2.2.1"
+	foundCorrectPackage := false
+	badVirtualPath := "/hudson.war:org.jvnet.hudson.main:hudson-war"
+	goodVirtualPath := "/hudson.war"
+	for _, p := range sbom.Artifacts.Packages.Sorted() {
+		if p.Type == pkg.JavaPkg && strings.Contains(p.Name, "hudson") {
+			assert.NotEqual(t, badPURL, p.PURL, "must not find bad purl %q", badPURL)
+			virtPath := ""
+			if meta, ok := p.Metadata.(pkg.JavaArchive); ok {
+				virtPath = meta.VirtualPath
+				if p.PURL == goodPURL && virtPath == goodVirtualPath {
+					foundCorrectPackage = true
+				}
+			}
+			assert.NotEqual(t, badVirtualPath, virtPath, "must not find bad virtual path %q", badVirtualPath)
+		}
+	}
+	assert.True(t, foundCorrectPackage, "must find correct package, but did not")
+}