Fix Go extractor incorrectly excluding packages with .. in relative paths

The Go extractor was incorrectly excluding valid packages when their relative
path from a wantedRoot contained '..' (parent directory references). This
occurred because the extractor checked each package against all wantedRoots,
and most sibling package directories resulted in relative paths like
'../../package/path' which matched the exclusion regex.

This fix introduces a priority root system that checks the module root and
package directory first before falling back to other roots. This ensures
packages are evaluated against the most relevant directories, avoiding false
positives from the '..' exclusion pattern.

Fixes packages being skipped during extraction when located in subdirectories
of a Go module, particularly affecting projects with vendor directories and
multiple nested package structures.

Author: allsmog

go/extractor/extractor.go

@@ -273,14 +273,33 @@ func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool)
 			return
 		}
 
-		for root := range wantedRoots {
-			pkgInfo := pkgInfos[pkg.PkgPath]
+		pkgInfo := pkgInfos[pkg.PkgPath]
+		matched := false
+
+		// Prioritize checking against module root and package directory.
+		// This avoids incorrectly excluding packages due to relative paths containing ".."
+		// when checking against unrelated sibling package directories.
+		priorityRoots := []string{}
+		if pkgInfo.ModDir != "" {
+			priorityRoots = append(priorityRoots, pkgInfo.ModDir)
+		}
+		priorityRoots = append(priorityRoots, pkgInfo.PkgDir)
+
+		for _, root := range priorityRoots {
+			if !wantedRoots[root] {
+				continue
+			}
+
 			relDir, err := filepath.Rel(root, pkgInfo.PkgDir)
-			if err != nil || noExtractRe.MatchString(relDir) {
-				// if the path can't be made relative or matches the noExtract regexp skip it
+			if err != nil {
+				continue
+			}
+
+			if relDir != "." && noExtractRe.MatchString(relDir) {
 				continue
 			}
 
+			matched = true
 			extraction.extractPackage(pkg)
 
 			modDir := pkgInfo.ModDir
@@ -306,7 +325,56 @@ func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool)
 			return
 		}
 
-		log.Printf("Skipping dependency package %s.", pkg.PkgPath)
+		// If priority roots didn't match, fall back to checking all other roots
+		if !matched {
+			for root := range wantedRoots {
+				// Skip priority roots we already checked
+				isPriorityRoot := false
+				for _, pr := range priorityRoots {
+					if root == pr {
+						isPriorityRoot = true
+						break
+					}
+				}
+				if isPriorityRoot {
+					continue
+				}
+
+				relDir, err := filepath.Rel(root, pkgInfo.PkgDir)
+				if err != nil || noExtractRe.MatchString(relDir) {
+					continue
+				}
+
+				matched = true
+				extraction.extractPackage(pkg)
+
+				modDir := pkgInfo.ModDir
+				if modDir == "" {
+					modDir = pkgInfo.PkgDir
+				}
+				if modDir != "" {
+					modPath := filepath.Join(modDir, "go.mod")
+					if util.FileExists(modPath) {
+						log.Printf("Extracting %s", modPath)
+						start := time.Now()
+
+						err := extraction.extractGoMod(modPath)
+						if err != nil {
+							log.Printf("Failed to extract go.mod: %s", err.Error())
+						}
+
+						end := time.Since(start)
+						log.Printf("Done extracting %s (%dms)", modPath, end.Nanoseconds()/1000000)
+					}
+				}
+
+				return
+			}
+		}
+
+		if !matched {
+			log.Printf("Skipping dependency package %s.", pkg.PkgPath)
+		}
 	})
 
 	extraction.WaitGroup.Wait()