Fix pre-commit hook path handling for projects in subdirectories

When the Gradle project root differs from the Git repository root
(e.g., Gradle is in a subdirectory like 'project/submodule/'), the pre-commit hooks
generated by ktlint-gradle fail to properly format files because of
path mismatches.

This change fixes the issue by:
- Using `git diff --relative=$gradleRootDirPrefix` to output paths
  relative to the Gradle project root
- Adding proper file path prefix handling in the git add command
  when checking if files exist and staging them

This ensures that when git outputs paths like "src/main/Foo.kt"
(relative to project/submodule/), the hook correctly references them as
"project/submodule/src/main/Foo.kt" when checking file existence and staging.

Fixes #374

Author: hey-cube

plugin/src/main/kotlin/org/jlleitschuh/gradle/ktlint/GitHook.kt

@@ -44,16 +44,18 @@ private fun generateGitCommand(
 ): String = if (gradleRootDirPrefix.isEmpty()) {
     "git --no-pager diff --name-status --no-color --cached"
 } else {
-    "git --no-pager diff --name-status --no-color --cached -- $gradleRootDirPrefix/"
+    "git --no-pager diff --name-status --no-color --cached --relative=$gradleRootDirPrefix -- $gradleRootDirPrefix/"
 }
 
 private fun postCheck(
-    shouldUpdateCommit: Boolean
+    shouldUpdateCommit: Boolean,
+    gradleRootDirPrefix: String
 ): String = if (shouldUpdateCommit) {
+    val filePrefix = if (gradleRootDirPrefix.isNotEmpty()) "$gradleRootDirPrefix/" else ""
     """
     echo "${'$'}CHANGED_FILES" | while read -r file; do
-        if [ -f ${'$'}file ]; then
-            git add ${'$'}file
+        if [ -f $filePrefix${'$'}file ]; then
+            git add $filePrefix${'$'}file
         fi
     done
     """
@@ -91,7 +93,7 @@ internal fun generateGitHook(
     gradle_command_exit_code=${'$'}?
 
     echo "Completed ktlint run."
-    ${postCheck(shouldUpdateCommit)}
+    ${postCheck(shouldUpdateCommit, gradleRootDirPrefix)}
 
     if [ -s ${'$'}diff ]; then
       git apply --ignore-whitespace ${'$'}diff