fix: convert file paths to workspace-relative paths

Author: WalterWoshid

src/main/kotlin/com/github/xepozz/mago/qualityTool/MagoAnnotatorProxy.kt

@@ -9,6 +9,9 @@ import com.intellij.psi.PsiFile
 import com.jetbrains.php.tools.quality.QualityToolAnnotator
 import com.jetbrains.php.tools.quality.QualityToolAnnotatorInfo
 import com.jetbrains.php.tools.quality.QualityToolConfiguration
+import java.io.File
+import java.nio.file.Path
+import java.nio.file.Paths
 
 open class MagoAnnotatorProxy : QualityToolAnnotator<MagoValidationInspection>() {
     companion object {
@@ -22,7 +25,8 @@ open class MagoAnnotatorProxy : QualityToolAnnotator<MagoValidationInspection>()
                 addConfig(project, settings)
 
                 add("fmt")
-                addAll(files)
+                files.map { toWorkspaceRelativePath(project, it) }
+                    .forEach { add(it) }
             }
                 .plus(ParametersList.parse(settings.formatAdditionalParameters))
                 .apply { println("format options: ${this.joinToString(" ")}") }
@@ -32,13 +36,45 @@ open class MagoAnnotatorProxy : QualityToolAnnotator<MagoValidationInspection>()
             addConfig(project, settings)
 
             add("analyze")
-            add(filePath)
+            add(toWorkspaceRelativePath(project, filePath))
             add("--reporting-format=json")
 //            filePath?.let { add(it) }
         }
             .plus(ParametersList.parse(settings.analyzeAdditionalParameters))
             .apply { println("analyze options: ${this.joinToString(" ")}") }
 
+        private fun toWorkspaceRelativePath(project: Project, rawFilePath: String): String {
+            val base = project.basePath ?: return ensureMagoPath(rawFilePath)
+
+            val relative = try {
+                val basePath: Path = Paths.get(base).normalize()
+                val filePath: Path = Paths.get(rawFilePath).normalize()
+
+                basePath.relativize(filePath).toString()
+            } catch (_: Throwable) {
+                rawFilePath
+            }
+            return ensureMagoPath(relative)
+        }
+
+        private fun ensureMagoPath(path: String): String {
+            if (path.isEmpty()) {
+                return path
+            }
+            return try {
+                if (Paths.get(path).isAbsolute) {
+                    path
+                } else if (path.startsWith("./") || path.startsWith(".\\")) {
+                    path
+                } else {
+                    // Mago ignores relative paths unless they are explicitly prefixed.
+                    ".${File.separator}$path"
+                }
+            } catch (_: Throwable) {
+                path
+            }
+        }
+
         private fun MutableList<String>.addWorkspace(project: Project) {
             val projectPath = updateIfRemoteMappingExists(
                 project.basePath ?: return,