1. In CommandAutofixAction.kt:

   - Refactored the `isGitignore` function to work with both `VirtualFile` and `Path` objects.
   - Improved the gitignore pattern matching logic.

2. In `GenerateDocumentationAction.kt`:
   - Enhanced the `transformContent` function to include project structure information in the API request.
   - Added a `findGitRoot` function to locate the Git root directory.
   - Improved the logic for generating individual output paths for documentation files.

3. In `TestResultAutofixAction.kt`:
   - Added a new `getFiles` function that works with `Path` objects.
   - Refactored the `getProjectStructure` function to work with both `VirtualFile` and `Path` objects.
   - Added a `findGitRoot` function that works with `Path` objects.

src/main/kotlin/com/github/simiacryptus/aicoder/actions/generic/CommandAutofixAction.kt

@@ -463,19 +463,21 @@ class CommandAutofixAction : BaseAction() {
     companion object {
         private val log = LoggerFactory.getLogger(CommandAutofixAction::class.java)
         val tripleTilde = "`" + "``" // This is a workaround for the markdown parser when editing this file
-        fun isGitignore(file: VirtualFile): Boolean {
-            var currentDir = file.toNioPath().toFile().parentFile
+        fun isGitignore(file: VirtualFile) = isGitignore(file.toNioPath())
+
+        fun isGitignore(path: Path): Boolean {
+            var currentDir = path.toFile().parentFile
             currentDir ?: return false
             while (!currentDir.resolve(".git").exists()) {
                 currentDir.resolve(".gitignore").let {
                     if (it.exists()) {
                         val gitignore = it.readText()
                         if (gitignore.split("\n").any { line ->
-                            val pattern = line.trim().trimEnd('/').replace(".", "\\.").replace("*", ".*")
-                            line.trim().isNotEmpty()
-                                    && !line.startsWith("#")
-                                    && file.name.trimEnd('/').matches(Regex(pattern))
-                        }) {
+                                val pattern = line.trim().trimEnd('/').replace(".", "\\.").replace("*", ".*")
+                                line.trim().isNotEmpty()
+                                        && !line.startsWith("#")
+                                        && path.fileName.toString().trimEnd('/').matches(Regex(pattern))
+                            }) {
                             return true
                         }
                     }
@@ -489,7 +491,7 @@ class CommandAutofixAction : BaseAction() {
                             val pattern = line.trim().trimEnd('/').replace(".", "\\.").replace("*", ".*")
                             line.trim().isNotEmpty()
                                     && !line.startsWith("#")
-                                    && file.name.trimEnd('/').matches(Regex(pattern))
+                                    && path.fileName.toString().trimEnd('/').matches(Regex(pattern))
                         }) {
                         return true
                     }

src/main/kotlin/com/github/simiacryptus/aicoder/actions/generic/GenerateDocumentationAction.kt

@@ -1,6 +1,7 @@
 package com.github.simiacryptus.aicoder.actions.generic
 
 import com.github.simiacryptus.aicoder.actions.FileContextAction
+import com.github.simiacryptus.aicoder.actions.test.TestResultAutofixAction.Companion.getProjectStructure
 import com.github.simiacryptus.aicoder.config.AppSettingsState
 import com.github.simiacryptus.aicoder.config.AppSettingsState.Companion.chatModel
 import com.github.simiacryptus.aicoder.config.Name
@@ -117,13 +118,21 @@ class GenerateDocumentationAction : FileContextAction<GenerateDocumentationActio
                     executorService.submit<Path?> {
                         val fileContent =
                             IOUtils.toString(FileInputStream(path.toFile()), "UTF-8") ?: return@submit null
-                        val transformContent = transformContent(fileContent, transformationMessage)
+                        val transformContent = transformContent(path, fileContent, transformationMessage)
                         if (config?.settings?.singleOutputFile == true) {
                             markdownContent.append("# ${root.relativize(path)}\n\n")
                             markdownContent.append(transformContent.replace("(?s)(?<![^\\n])#".toRegex(), "\n##"))
                         } else {
-                            root.relativize(path).let { it.parent.resolve(it.fileName.toString().split('.').dropLast(1).joinToString(".") + "_" + outputPath.fileName) }
-                            val individualOutputPath = root.resolve("${root.relativize(path)}.md")
+                            val individualOutputPath = root.resolve(
+                                "${
+                                    root.relativize(
+                                        path.parent.resolve(
+                                            path.fileName.toString().split('.').dropLast(1)
+                                                .joinToString(".") + "." + outputPath.fileName
+                                        )
+                                    )
+                                }.md"
+                            )
                             Files.write(individualOutputPath, transformContent.toByteArray())
                         }
                         path
@@ -149,23 +158,46 @@ class GenerateDocumentationAction : FileContextAction<GenerateDocumentationActio
         }
     }
 
-    private fun transformContent(fileContent: String, transformationMessage: String) = api.chat(
+    private fun transformContent(path: Path, fileContent: String, transformationMessage: String) = api.chat(
         ApiModel.ChatRequest(
             model = AppSettingsState.instance.smartModel.chatModel().modelName,
             temperature = AppSettingsState.instance.temperature,
             messages = listOf(
                 ApiModel.ChatMessage(
                     ApiModel.Role.system, """
-            You will combine natural language instructions with a user provided code example to document code.
-            """.trimIndent().toContentList(), null
+                        You will combine natural language instructions with a user provided code example to document code.
+                        """.trimIndent().toContentList(), null
+                ),
+                ApiModel.ChatMessage(
+                    ApiModel.Role.user,
+                    """
+                    |## Project:
+                    |${findGitRoot(path)?.let { getProjectStructure(it) }}
+                    |
+                    |## $path:
+                    |```
+                    |$fileContent
+                    |```
+                    |
+                    |Instructions: $transformationMessage
+                    """.trimMargin().toContentList()
                 ),
-                ApiModel.ChatMessage(ApiModel.Role.user, fileContent.toContentList()),
-                ApiModel.ChatMessage(ApiModel.Role.user, transformationMessage.toContentList()),
             ),
         ),
         AppSettingsState.instance.smartModel.chatModel()
     ).choices.first().message?.content?.trim() ?: fileContent
 
+    fun findGitRoot(path: Path?): Path? {
+        var current: Path? = path
+        while (current != null) {
+            if (current.resolve(".git").toFile().exists()) {
+                return current
+            }
+            current = current.parent
+        }
+        return null
+    }
+
     companion object {
         private val scheduledPool = Executors.newScheduledThreadPool(1)
         fun open(project: Project, outputPath: Path) {

src/main/kotlin/com/github/simiacryptus/aicoder/actions/test/TestResultAutofixAction.kt

@@ -54,11 +54,28 @@ class TestResultAutofixAction : BaseAction() {
             }
             return codeFiles
         }
+        fun getFiles(
+            virtualFiles: Array<out Path>?
+        ): MutableSet<Path> {
+            val codeFiles = mutableSetOf<Path>()    // Set to avoid duplicates
+            virtualFiles?.forEach { file ->
+                if(file.fileName.startsWith(".")) return@forEach
+                if(CommandAutofixAction.isGitignore(file)) return@forEach
+                if (file.toFile().isDirectory) {
+                    codeFiles.addAll(getFiles(file.toFile().listFiles().map { it.toPath() }.toTypedArray()))
+                } else {
+                    codeFiles.add(file)
+                }
+            }
+            return codeFiles
+        }
+
         fun getProjectStructure(projectPath: VirtualFile?): String {
-            if (projectPath == null) return "Project path is null"
-            val root = Path.of(projectPath!!.path)
+            return getProjectStructure(Path.of((projectPath?: return "Project path is null").path))
+        }
 
-            val codeFiles = getFiles(arrayOf(projectPath!!))
+        fun getProjectStructure(root: Path): String {
+            val codeFiles = getFiles(arrayOf(root))
                 .filter { it.toFile().length() < 1024 * 1024 / 2 } // Limit to 0.5MB
                 .map { root.relativize(it) ?: it }.toSet()
             val str = codeFiles
@@ -71,6 +88,17 @@ class TestResultAutofixAction : BaseAction() {
             return str
         }
 
+        fun findGitRoot(path: Path?): Path? {
+            var current: Path? = path
+            while (current != null) {
+                if (current.resolve(".git").toFile().exists()) {
+                    return current
+                }
+                current = current.parent
+            }
+            return null
+        }
+
         fun findGitRoot(virtualFile: VirtualFile?): VirtualFile? {
             var current: VirtualFile? = virtualFile
             while (current != null) {