fix(go): handle replace directives in go list -m all parsing (#468)

## Summary
- Fix `go list -m all` parsing in
`GoModulesProvider.getFinalPackagesVersionsForModule()` to handle Go
replace directives (5-part format: `name v1 => replacement v2`)
- Extract `parseModuleVersions()` method mirroring JS client PR #505
- Add replace directive test fixture to `go_mod_light_no_ignore` and
update expected SBOM

Implements [TC-4359](https://redhat.atlassian.net/browse/TC-4359)

## Test plan
- [x] All 18 Go module tests pass (all 6 parameterized folders, both
stack and component analysis)
- [x] `go_mod_no_path` fixture with no-op replace still passes
- [x] MVS-related tests pass (`Test_Golang_MvS_Logic_Disabled`,
`Test_Golang_MvS_Enabled_Preserves_All_Transitive_Dependencies`)
- [x] `mvn spotless:apply` passes (code formatted)
- [x] `mvn verify` passes (only pre-existing Python env failures)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

[TC-4359]:
https://redhat.atlassian.net/browse/TC-4359?atlOrigin=eyJpIjoiNWRkNTljNzYxNjVmNDY3MDlhMDU5Y2ZhYzA5YTRkZjUiLCJwIjoiZ2l0aHViLWNvbS1KU1cifQ

## Summary by Sourcery

Handle Go module replace directives when resolving final package
versions from `go list -m all` output.

Bug Fixes:
- Correct resolution of final Go module versions by supporting replace
directive lines in `go list -m all` output.

Enhancements:
- Extract shared `parseModuleVersions` helper to parse `go list -m all`
output into a module-to-version map.

Tests:
- Extend Go module test fixtures with a replace directive example and
update the expected SBOM for stack analysis to cover the new behavior.

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: a-oren

src/main/java/io/github/guacsec/trustifyda/providers/GoModulesProvider.java

@@ -347,12 +347,7 @@ private Map<String, List<String>> getFinalPackagesVersionsForModule(
     Operations.runProcessGetOutput(manifestPath.getParent(), goExecutable, "mod", "download");
     String finalVersionsForAllModules =
         Operations.runProcessGetOutput(manifestPath.getParent(), goExecutable, "list", "-m", "all");
-    Map<String, String> finalModulesVersions =
-        Arrays.stream(finalVersionsForAllModules.split(Operations.GENERIC_LINE_SEPARATOR))
-            .filter(string -> string.trim().split(" ").length == 2)
-            .collect(
-                Collectors.toMap(
-                    t -> t.split(" ")[0], t -> t.split(" ")[1], (first, second) -> second));
+    Map<String, String> finalModulesVersions = parseModuleVersions(finalVersionsForAllModules);
     Map<String, List<String>> listWithModifiedVersions = new HashMap<>();
     // Process all entries, including those without versions (like the root module)
     edges.forEach(
@@ -387,6 +382,25 @@ private Map<String, List<String>> getFinalPackagesVersionsForModule(
     return listWithModifiedVersions;
   }
 
+  /**
+   * Parses {@code go list -m all} output into a map of module names to their final resolved
+   * versions. Handles both standard lines ({@code name version}) and replace directive lines
+   * ({@code name v1 => replacement v2}).
+   */
+  static Map<String, String> parseModuleVersions(String goListOutput) {
+    return Arrays.stream(goListOutput.split(Operations.GENERIC_LINE_SEPARATOR))
+        .map(String::trim)
+        .filter(line -> !line.isEmpty())
+        .map(line -> line.split("\\s+"))
+        .filter(parts -> parts.length == 2 || (parts.length >= 4 && parts[2].equals("=>")))
+        .collect(
+            Collectors.toMap(
+                parts -> parts[0],
+                parts ->
+                    parts.length >= 4 && parts[2].equals("=>") ? parts[parts.length - 1] : parts[1],
+                (first, second) -> second));
+  }
+
   private List<String> getListOfPackagesWithFinalVersions(
       Map<String, String> finalModulesVersions, List<String> packages) {
     return packages.stream()

src/test/java/io/github/guacsec/trustifyda/providers/GoModulesParseModuleVersionsTest.java

@@ -0,0 +1,86 @@
+/*
+ * Copyright 2023-2025 Trustify Dependency Analytics Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.github.guacsec.trustifyda.providers;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.util.Map;
+import org.junit.jupiter.api.Test;
+
+class GoModulesParseModuleVersionsTest {
+
+  @Test
+  void parseStandardModuleLines() {
+    String input = "github.com/foo/bar v1.2.3\ngithub.com/baz/qux v0.1.0\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result)
+        .containsEntry("github.com/foo/bar", "v1.2.3")
+        .containsEntry("github.com/baz/qux", "v0.1.0")
+        .hasSize(2);
+  }
+
+  @Test
+  void parseReplaceDirectiveLines() {
+    String input = "github.com/old/mod v1.0.0 => github.com/new/mod v2.0.0\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result).containsEntry("github.com/old/mod", "v2.0.0").hasSize(1);
+  }
+
+  @Test
+  void parseWithMultipleSpacesAndTabs() {
+    String input = "github.com/foo/bar   v1.2.3\ngithub.com/baz/qux\tv0.1.0\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result)
+        .containsEntry("github.com/foo/bar", "v1.2.3")
+        .containsEntry("github.com/baz/qux", "v0.1.0")
+        .hasSize(2);
+  }
+
+  @Test
+  void parseWithBlankAndWhitespaceOnlyLines() {
+    String input = "\n  \ngithub.com/foo/bar v1.0.0\n\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result).containsEntry("github.com/foo/bar", "v1.0.0").hasSize(1);
+  }
+
+  @Test
+  void parseSkipsMalformedLines() {
+    String input = "github.com/foo/bar v1.0.0\nsingle-token\nthree tokens here\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result).containsEntry("github.com/foo/bar", "v1.0.0").hasSize(1);
+  }
+
+  @Test
+  void parseEmptyInput() {
+    Map<String, String> result = GoModulesProvider.parseModuleVersions("");
+    assertThat(result).isEmpty();
+  }
+
+  @Test
+  void parseReplaceDirectiveWithTabSeparation() {
+    String input = "github.com/old/mod\tv1.0.0\t=>\tgithub.com/new/mod\tv2.0.0\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result).containsEntry("github.com/old/mod", "v2.0.0").hasSize(1);
+  }
+
+  @Test
+  void parseDuplicateModuleKeepsLast() {
+    String input = "github.com/foo/bar v1.0.0\ngithub.com/foo/bar v2.0.0\n";
+    Map<String, String> result = GoModulesProvider.parseModuleVersions(input);
+    assertThat(result).containsEntry("github.com/foo/bar", "v2.0.0").hasSize(1);
+  }
+}

src/test/resources/tst_manifests/golang/go_mod_light_no_ignore/expected_sbom_stack_analysis.json

@@ -263,11 +263,11 @@
     },
     {
       "type": "library",
-      "bom-ref": "pkg:golang/gopkg.in/yaml.v3@v3.0.1",
+      "bom-ref": "pkg:golang/gopkg.in/yaml.v3@v3.0.0",
       "group": "gopkg.in",
       "name": "yaml.v3",
-      "version": "v3.0.1",
-      "purl": "pkg:golang/gopkg.in/yaml.v3@v3.0.1"
+      "version": "v3.0.0",
+      "purl": "pkg:golang/gopkg.in/yaml.v3@v3.0.0"
     },
     {
       "type": "library",
@@ -497,7 +497,7 @@
       "dependsOn": []
     },
     {
-      "ref": "pkg:golang/gopkg.in/yaml.v3@v3.0.1",
+      "ref": "pkg:golang/gopkg.in/yaml.v3@v3.0.0",
       "dependsOn": [
         "pkg:golang/gopkg.in/check.v1@v0.0.0-20161208181325-20d25e280405"
       ]

src/test/resources/tst_manifests/golang/go_mod_light_no_ignore/go.mod

@@ -6,3 +6,5 @@ require golang.org/x/tools v0.0.0-20210112183307-1e6ecd4bf1b0
 require github.com/spf13/cobra v0.0.5
 
 require gopkg.in/yaml.v3 v3.0.1 // indirect
+
+replace gopkg.in/yaml.v3 v3.0.1 => gopkg.in/yaml.v3 v3.0.0