dev, kernel, tools, tooling, tex: add mk_app tool, see details.

	- Patch HeFS implementation file, working on a allocation
	  function now.
	- Generated LaTeX specs from source code.
	- Add mk.{hefs, nefs} tools for future formatting (with diutil
	  first)
	- Add python tool to generate user apps for NeKernel.

Signed-off-by: Amlal El Mahrouss <amlal@nekernel.org>

11 files changed, 284 insertions, 47 deletions

diff --git a/dev/kernel/src/FS/HeFS.cc b/dev/kernel/src/FS/HeFS.cc
index 142ddbea..8d73b61e 100644
--- a/dev/kernel/src/FS/HeFS.cc
+++ b/dev/kernel/src/FS/HeFS.cc
@@ -15,6 +15,7 @@
 #include <NewKit/KString.h>
 #include <NewKit/Utils.h>
 #include <FirmwareKit/EPM.h>
+#include <FirmwareKit/GPT.h>
 #include <KernelKit/ProcessScheduler.h>
 #include <KernelKit/User.h>
 
@@ -22,7 +23,30 @@ namespace Kernel
 {
 	namespace Detail
 	{
-		STATIC HEFS_INDEX_NODE* hefs_get_index_node(HEFS_BOOT_NODE* root, DriveTrait* mnt, const Utf16Char* dir_name, const Utf16Char* file_name, UInt8 kind) noexcept
+		/// @brief Forward declarations of internal functions.
+
+		/// @brief Get the index node of a file or directory.
+		/// @param root The root node of the filesystem.
+		/// @param mnt The drive to read from.
+		/// @param dir_name The name of the directory.
+		/// @param file_name The name of the file.
+		/// @param kind The kind of the file (regular, directory, block, character, FIFO, socket, symbolic link, unknown).
+		STATIC HEFS_INDEX_NODE* hefs_fetch_index_node(HEFS_BOOT_NODE* root, DriveTrait* mnt, const Utf16Char* dir_name, const Utf16Char* file_name, UInt8 kind) noexcept;
+
+		/// @brief Allocate a new index node.
+		/// @param root The root node of the filesystem.
+		/// @param mnt The drive to read from.
+		/// @param parent_dir_name The name of the parent directory.
+		/// @return Status, see err_global_get().
+		STATIC BOOL hefs_allocate_index_node(HEFS_BOOT_NODE* root, DriveTrait* mnt, const Utf16Char* parent_dir_name, HEFS_INDEX_NODE* node) noexcept;
+
+		/// @brief Get the index node of a file or directory.
+		/// @param root The root node of the filesystem.
+		/// @param mnt The drive to read from.
+		/// @param dir_name The name of the directory.
+		/// @param file_name The name of the file.
+		/// @param kind The kind of the file (regular, directory, block, character, FIFO, socket, symbolic link, unknown).
+		STATIC HEFS_INDEX_NODE* hefs_fetch_index_node(HEFS_BOOT_NODE* root, DriveTrait* mnt, const Utf16Char* dir_name, const Utf16Char* file_name, UInt8 kind) noexcept
 		{
 			if (root)
 			{
@@ -42,10 +66,9 @@ namespace Kernel
 
 				while (start != end)
 				{
-					if (hop_watch++ > 100)
+					if (hop_watch > 100)
 					{
-						kout << "Error: Hop watch exceeded.\r";
-
+						kout << "Error: Hop watch exceeded, filesystem is stalling.\r";
 						break;
 					}
 
@@ -66,8 +89,10 @@ namespace Kernel
 						delete node;
 						delete dir;
 
-						err_global_get() = kErrorFileNotFound;
+						dir	 = nullptr;
+						node = nullptr;
 
+						err_global_get() = kErrorFileNotFound;
 
 						return nullptr;
 					}
@@ -78,9 +103,10 @@ namespace Kernel
 						{
 							for (SizeT inode_index = 0UL; inode_index < kHeFSBlockCount; ++inode_index)
 							{
-								if (dir->fIndexNodeStart[inode_index] != 0)
+								if (dir->fIndexNodeStart[inode_index] != 0 ||
+									dir->fIndexNodeEnd[inode_index] != 0)
 								{
-									mnt->fPacket.fPacketLba		= dir->fIndexNodeStart[inode_index];
+									mnt->fPacket.fPacketLba		= (!dir->fIndexNodeStart[inode_index]) ? dir->fIndexNodeEnd[inode_index] : dir->fIndexNodeStart[inode_index];
 									mnt->fPacket.fPacketSize	= sizeof(HEFS_INDEX_NODE);
 									mnt->fPacket.fPacketContent = node;
 
@@ -91,35 +117,22 @@ namespace Kernel
 										if (KStringBuilder::Equals(file_name, node->fName) && node->fKind == kind)
 										{
 											delete dir;
+											dir = nullptr;
 
 											return node;
 										}
 									}
 									else
 									{
-										break;
-									}
-								}
-								else if (dir->fIndexNodeEnd[inode_index] != 0)
-								{
-									mnt->fPacket.fPacketLba		= dir->fIndexNodeEnd[inode_index];
-									mnt->fPacket.fPacketSize	= sizeof(HEFS_INDEX_NODE);
-									mnt->fPacket.fPacketContent = node;
+										err_global_get() = kErrorDiskIsCorrupted;
 
-									mnt->fInput(mnt->fPacket);
+										delete dir;
+										delete node;
 
-									if (mnt->fPacket.fPacketGood)
-									{
-										if (KStringBuilder::Equals(file_name, node->fName) && node->fKind == kind)
-										{
-											delete dir;
+										dir	 = nullptr;
+										node = nullptr;
 
-											return node;
-										}
-									}
-									else
-									{
-										break;
+										return nullptr;
 									}
 								}
 							}
@@ -148,6 +161,21 @@ namespace Kernel
 
 			return nullptr;
 		}
+
+		/// @brief Allocate a new index node.
+		/// @param root The root node of the filesystem.
+		/// @param mnt The drive to read from.
+		/// @param parent_dir_name The name of the parent directory.
+		/// @return Status, see err_global_get().
+		STATIC BOOL hefs_allocate_index_node(HEFS_BOOT_NODE* root, DriveTrait* mnt, const Utf16Char* parent_dir_name, HEFS_INDEX_NODE* node) noexcept
+		{
+			NE_UNUSED(root);
+			NE_UNUSED(mnt);
+			NE_UNUSED(parent_dir_name);
+			NE_UNUSED(node);
+			
+			return NO;
+		}
 	} // namespace Detail
 } // namespace Kernel
 
diff --git a/docs/tex/hefs.tex b/docs/tex/hefs.tex
index e74cf5e3..3370af48 100644
--- a/docs/tex/hefs.tex
+++ b/docs/tex/hefs.tex
@@ -1,32 +1,123 @@
 \documentclass{article}
-\usepackage[a4paper,margin=1in]{geometry}
+\usepackage[a4paper, margin=1in]{geometry}
+\usepackage{amsmath, amssymb}
 \usepackage{listings}
 \usepackage{xcolor}
-\usepackage{amsmath}
-\usepackage{hyperref}
-\usepackage{longtable}
-\usepackage{titlesec}
-\usepackage{fancyhdr}
-\usepackage{caption}
 \usepackage{graphicx}
+\usepackage{enumitem}
+\usepackage{caption}
+\usepackage{longtable}
 
-\definecolor{codegray}{gray}{0.95}
-\lstset{
-  backgroundcolor=\color{codegray},
+\definecolor{lightgray}{gray}{0.95}
+
+\lstdefinestyle{cstyle}{
+  language=C++,
+  backgroundcolor=\color{lightgray},
   basicstyle=\ttfamily\small,
+  keywordstyle=\color{blue},
+  commentstyle=\color{green!60!black},
+  stringstyle=\color{orange},
+  numbers=left,
+  numberstyle=\tiny,
   breaklines=true,
   frame=single,
-  tabsize=4,
-  language=C++,
   showstringspaces=false
 }
 
-\title{HeFS: High-Throughput Extended File System Specification}
+\title{HeFS (Hierarchical Embedded File System) Specification}
 \author{Amlal El Mahrouss}
-\date{2025}
+\date{2024–2025}
 
 \begin{document}
 
 \maketitle
 
-\end{document}
+\section{Overview}
+HeFS is a custom filesystem developed as part of the NeKernel project. It offers a journaling-like inode tree structure using red-black tree-inspired navigation for directories. Designed for robust use in desktop and server workloads, it supports various encoding modes and drive types.
+
+\section{Boot Node Structure}
+\begin{longtable}{|l|l|p{8cm}|}
+\hline
+\textbf{Field} & \textbf{Type} & \textbf{Description} \\
+\hline
+\verb|fMagic| & \verb|char[8]| & Filesystem magic ("  HeFS") \\
+\verb|fVolName| & \verb|Utf16Char[128]| & Volume name \\
+\verb|fVersion| & \verb|UInt32| & Filesystem version (e.g., 0x0100) \\
+\verb|fSectorCount| & \verb|UInt64| & Total sector count \\
+\verb|fSectorSize| & \verb|UInt64| & Size of each sector \\
+\verb|fDriveKind| & \verb|UInt8| & Type of drive (e.g., HDD, SSD, USB) \\
+\verb|fEncoding| & \verb|UInt8| & Encoding mode (UTF-8, UTF-16, etc.) \\
+\verb|fStartIND| & \verb|UInt64| & Starting LBA of inode tree \\
+\verb|fEndIND| & \verb|UInt64| & Ending LBA of inode tree \\
+\verb|fChecksum| & \verb|UInt32| & CRC32 of boot node \\
+\verb|fDiskSize| & \verb|UInt64| & Logical size of the disk \\
+\hline
+\end{longtable}
+
+\section{File Types and Flags}
+\subsection*{File Kinds}
+\begin{itemize}[label=--]
+    \item \verb|0x00| — Regular File
+    \item \verb|0x01| — Directory
+    \item \verb|0x02| — Block Device
+    \item \verb|0x03| — Character Device
+    \item \verb|0x04| — FIFO
+    \item \verb|0x05| — Socket
+    \item \verb|0x06| — Symbolic Link
+\end{itemize}
+
+\subsection*{Drive Types}
+\begin{itemize}[label=--]
+    \item \verb|0xC0| — Hard Drive
+    \item \verb|0xC1| — SSD
+    \item \verb|0xCC| — Mass Storage Device (USB)
+\end{itemize}
+
+\section{Index Node Structure}
+The inode tree allows for fast access and recovery via dual start/end block mappings and timestamped metadata.
+
+\begin{lstlisting}[style=cstyle, caption={HEFS\_INDEX\_NODE structure}]
+struct HEFS_INDEX_NODE {
+    Utf16Char fName[256];
+    UInt32    fFlags;
+    UInt16    fKind;
+    UInt32    fSize;
+    UInt32    fChecksum, fRecoverChecksum, fBlockChecksum, fLinkChecksum;
+    ATime     fCreated, fAccessed, fModified, fDeleted;
+    UInt32    fUID, fGID;
+    UInt32    fMode;
+    UInt64    fBlockLinkStart[16], fBlockLinkEnd[16];
+    UInt64    fBlockStart[16], fBlockEnd[16];
+    UInt64    fBlockRecoveryStart[16], fBlockRecoveryEnd[16];
+};
+\end{lstlisting}
+
+\section{Directory Node Structure}
+Each directory is a red-black tree node with child and sibling pointers.
+
+\begin{lstlisting}[style=cstyle, caption={HEFS\_INDEX\_NODE\_DIRECTORY structure}]
+struct HEFS_INDEX_NODE_DIRECTORY {
+    Utf16Char fName[256];
+    UInt32 fFlags;
+    UInt16 fKind;
+    UInt32 fSize;
+    UInt32 fChecksum, fIndexNodeChecksum;
+    ATime  fCreated, fAccessed, fModified, fDeleted;
+    UInt32 fUID, fGID;
+    UInt32 fMode;
+    UInt64 fIndexNodeStart[16], fIndexNodeEnd[16];
+    UInt8  fColor;
+    Lba    fNext, fPrev, fChild, fParent;
+};
+\end{lstlisting}
+
+\section{Future Work}
+Planned extensions include:
+\begin{itemize}
+    \item Journaling recovery logic
+    \item Advanced permission flags
+    \item Logical volume management support
+    \item Cross-filesystem linking (EPM integration)
+\end{itemize}
+
+\end{document}
\ No newline at end of file
diff --git a/public/tools/diutil/src/CommandLine.cc b/public/tools/diutil/src/CommandLine.cc
index 604520a9..3e7353e6 100644
--- a/public/tools/diutil/src/CommandLine.cc
+++ b/public/tools/diutil/src/CommandLine.cc
@@ -9,12 +9,12 @@
 
 #include <DiskImage.fwrk/headers/DiskImage.h>
 
-static const Char kDiskName[kDIDiskNameLen] = "Disk";
-static SInt32	  kDiskSectorSz				= 512;
+static const Char kDiskName[kDIDiskNameLen] = "DISK";
+static SInt32	  kDiskSectorSz				= kDISectorSz;
 static SizeT	  kDiskSz					= gib_cast(4);
 static const Char kOutDisk[kDIOutNameLen]	= "disk.eimg";
 
-/// @brief Filesystem tool entrypoint.
+/// @brief Disk Utility entrypoint.
 int main(int argc, char** argv)
 {
 	for (SInt32 arg = 0; arg < argc; ++arg)
diff --git a/public/tools/mk.hefs/.keep b/public/tools/mk.hefs/.keep
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/public/tools/mk.hefs/.keep
diff --git a/public/tools/mk.hefs/mk.hefs.json b/public/tools/mk.hefs/mk.hefs.json
new file mode 100644
index 00000000..03f925cf
--- /dev/null
+++ b/public/tools/mk.hefs/mk.hefs.json
@@ -0,0 +1,12 @@
+{
+  "compiler_path": "g++",
+  "compiler_std": "c++20",
+  "headers_path": ["./", "../../../dev"],
+  "sources_path": ["src/CommandLine.cc"],
+  "output_name": "./dist/mk.hefs",
+  "cpp_macros": [
+    "kCCVersion=0x0100",
+    "kCCVersionHighest=0x0100",
+    "kCCVersionLowest=0x0100"
+  ]
+}
diff --git a/public/tools/mk.hefs/src/CommandLine.cc b/public/tools/mk.hefs/src/CommandLine.cc
new file mode 100644
index 00000000..23681be8
--- /dev/null
+++ b/public/tools/mk.hefs/src/CommandLine.cc
@@ -0,0 +1,14 @@
+/*
+ * Created on Thu Oct 17 08:00:42 CEST 2024
+ *
+ * Copyright (c) 2025 Amlal El Mahrouss
+ */
+
+#include <user/SystemCalls.h>
+
+/// @brief Placeholder program.
+
+SInt32 main(SInt32 argc, Char* argv[])
+{
+	return EXIT_FAILURE;
+}
diff --git a/public/tools/mk.nefs/.keep b/public/tools/mk.nefs/.keep
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/public/tools/mk.nefs/.keep
diff --git a/public/tools/mk.nefs/mk.nefs.json b/public/tools/mk.nefs/mk.nefs.json
new file mode 100644
index 00000000..e92e0b9c
--- /dev/null
+++ b/public/tools/mk.nefs/mk.nefs.json
@@ -0,0 +1,12 @@
+{
+  "compiler_path": "g++",
+  "compiler_std": "c++20",
+  "headers_path": ["./", "../../../dev"],
+  "sources_path": ["src/CommandLine.cc"],
+  "output_name": "./dist/mk.nefs",
+  "cpp_macros": [
+    "kCCVersion=0x0100",
+    "kCCVersionHighest=0x0100",
+    "kCCVersionLowest=0x0100"
+  ]
+}
diff --git a/public/tools/mk.nefs/src/CommandLine.cc b/public/tools/mk.nefs/src/CommandLine.cc
new file mode 100644
index 00000000..23681be8
--- /dev/null
+++ b/public/tools/mk.nefs/src/CommandLine.cc
@@ -0,0 +1,14 @@
+/*
+ * Created on Thu Oct 17 08:00:42 CEST 2024
+ *
+ * Copyright (c) 2025 Amlal El Mahrouss
+ */
+
+#include <user/SystemCalls.h>
+
+/// @brief Placeholder program.
+
+SInt32 main(SInt32 argc, Char* argv[])
+{
+	return EXIT_FAILURE;
+}
diff --git a/tooling/mk_app.py b/tooling/mk_app.py
new file mode 100755
index 00000000..34a7702e
--- /dev/null
+++ b/tooling/mk_app.py
@@ -0,0 +1,67 @@
+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import json
+import sys
+
+def create_directory_structure(base_path, project_name):
+    # Define the directory structure
+    structure = {
+        project_name: {
+            "src": {
+                ".keep": None
+            },
+            "vendor": {
+                ".keep": None
+            },
+            ".keep": None,
+            f"{project_name}.json": {}
+        }
+    }
+
+    def create_structure(path, structure):
+        for name, content in structure.items():
+            current_path = os.path.join(path, name)
+            # Create directories or files based on the content type
+            if isinstance(content, dict) and current_path.endswith(".json") == False:
+                os.makedirs(current_path, exist_ok=True)
+                create_structure(current_path, content)
+            elif content is None:
+                # Create an empty file
+                with open(current_path, 'w') as f:
+                    pass
+
+    # Create the base directory
+    os.makedirs(base_path, exist_ok=True)
+    create_structure(base_path, structure)
+
+    # Create the JSON file
+    diutil_json_path = os.path.join(base_path, project_name, f"{project_name}.json")
+    manifest = {
+        "compiler_path": "g++",
+        "compiler_std": "c++20",
+        "headers_path": ["./", "../../../dev/kernel", "../../../public/frameworks/", "../../../dev/", "./"],
+        "sources_path": [
+            
+        ],
+        "output_name": f"./dist/{project_name}",
+        "cpp_macros": [
+            "kSampleVersion=0x0100",
+            "kSampleVersionHighest=0x0100",
+            "kSampleVersionLowest=0x0100",
+            "__NE_SDK__"
+        ]
+    }
+    
+    with open(diutil_json_path, 'w') as json_file:
+        json.dump(manifest, json_file, indent=4)
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        print("Usage: mk_app.py <project_name>")
+        sys.exit(1)
+
+    base_path = os.getcwd()  # Use the current working directory as the base path
+    create_directory_structure(base_path, sys.argv[1])
+    print("Ne application created successfully.")
\ No newline at end of file
diff --git a/tooling/copy_to_fat32.py b/tooling/mk_img.py
index ea0cb1b9..253e5a6c 100755
--- a/tooling/copy_to_fat32.py
+++ b/tooling/mk_img.py
@@ -17,7 +17,6 @@ def copy_to_fat(image_path, source_dir):
 
     try:
         files_to_copy = glob.glob(os.path.join(source_dir, "*"))
-
         # Now build the command
         command = ["mcopy", "-spom", "-i", image_path] + files_to_copy + ["::"]
         subprocess.run(command, check=True)
@@ -35,7 +34,7 @@ def copy_to_fat(image_path, source_dir):
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:
-        print("Usage: python3 copy_to_fat32.py <fat32_image> <source_directory>")
+        print("Usage: mk_img.py <fat32_image> <source_directory>")
         sys.exit(1)
 
     image_path = sys.argv[1]