Теперь коммиты создаются корректно, не перекрывают состояния файлов друг друга.

При создании коммитов происходит проверка на наличие последнего коммита в ветке и, если коммит не является последним - то происходит ответвление "текущая дата" + "текущий коммит".
Небольшой рефакторинг.

source/snag/core/core.d

@@ -2,6 +2,7 @@ module snag.core.core;
 
 import snag.config;
 import std.format;
+import std.datetime : Clock;
 import std.stdio;
 import std.array;
 import std.process;
@@ -14,6 +15,7 @@ import snag.core.exception;
 class Snag {
 	private string[] _baseCommand;
 	private SnagConfig _config;
+	private string _date;
 
 	private bool isValidHash(string hash) {
 		auto hashPattern = ctRegex!r"^[a-fA-F0-9]{7}$";
@@ -26,6 +28,15 @@ class Snag {
 			config.git, config.project
 		).split();
 		_config = config;
+
+		auto currentTime = Clock.currTime();
+
+		_date = format("%02d%03d%02d%02d%02d",
+						currentTime.year % 100,
+						currentTime.dayOfYear,
+						currentTime.hour,
+						currentTime.minute,
+						currentTime.second);
 	}
 
 	private auto git(string[] command, string message, string separator = ":\n") {
@@ -51,8 +62,8 @@ class Snag {
 			"A Git repository initialization error occurred"
 		);
 		writeln(
-			"The Git repository has been initialized successfully: "
+			"The Git repository has been initialized successfully: ",
-			~ _config.git
+			_config.git
 		);
 	}
 
@@ -62,8 +73,12 @@ class Snag {
 			"An error occurred while checking the file tracking status"
 		);
 
-		writeln("The following list of files requires backup:");
+		if (!result.output.length) {
+			writeln("The current state of the files is up to date as of the latest snapshot");
+			return;
+		}
 
+		writeln("The following list of files requires backup:");
 		result.output.split('\n').filter!(e => !e.strip.empty).each!((e) {
 			writefln("\t/%s", e.strip.split[1]);
 		});
@@ -75,6 +90,7 @@ class Snag {
 			"An error occurred while checking the file tracking status"
 		);
 
+		// Если нечего коммитить, то выходим
 		if (!result.output.length)
 			throw new SnagException(
 				"Current file state doesn't need to be archived again"
@@ -82,6 +98,7 @@ class Snag {
 
 		result = execute(_baseCommand ~ ["rev-parse", "--short", "HEAD"]);
 		if (result.status == 128) {
+			// Если это самый первый коммит после инициализации репозитория
 			git(["add", "."], "Failed to prepare files for archiving");
 			git(["commit", "-m", "test"], "Failed to create a backup");
 			writeln("Backup was created successfully");
@@ -92,56 +109,76 @@ class Snag {
 				~ result.output
 			);
 
+		// Текущий коммит, который был изменен
 		string currentSnapshot = result.output.strip('\n');
 
-		git(
+		// Если текущий измененный коммит является последним в ветке - то продолжить коммиты в этой ветке
-			["checkout", "-b", "mod", currentSnapshot ],
+		string currentBranch = git(
-			"Failed to create a branch from the current state"
+			["for-each-ref", "--contains", currentSnapshot, "--format='%(refname:short)'"],
-		);
+			"Error while getting the current branch"
-		git(
+		).output.split('\n')[0].strip('\'');
-			["add", "."],
-			"Failed to prepare files for archiving"
-		);
-		git(
-			["commit", "-m", "test"],
-			"Failed to create a backup"
-		);
-		git(
-			["checkout", "master"],
-			"Failed to perform intermediate state switching"
-		);
-		git(
-			["rebase", "--onto", "mod", currentSnapshot, "master", "-X", "theirs"],
-			"Ошибка при rebase"
-		);
 
+		// Получение списка коммитов между текущим и веткой
 		result = git(
-			["rev-parse", "--short", "mod"],
+			["log", "--oneline", "HEAD.." ~ currentBranch],
-			"An error occurred while checking the file tracking status"
+			"Failed to get the commit list between HEAD and " ~ currentBranch
 		);
 
-		string newSnapshot = result.output.strip('\n');
+		string newSnapshot;
 
-		git(
+		// Если список существует
-			["checkout", newSnapshot],
+		if (result.output.length) {
-			"Failed to perform intermediate state switching"
+			// Если коммит не является последним, то необходимо ответвление
-		);
+			string newBranch = "%s-%s".format(_date, currentSnapshot);
-		git(
+			git(
-			["branch", "-D", "mod"],
+				["checkout", "-b", newBranch, currentSnapshot ],
-			"Error while deleting temporary intermediate snapshot"
+				"Failed to create a branch from the current state"
-		);
+			);
-		writeln("Backup was created successfully");
+			git(
+				["add", "."],
+				"Failed to prepare files for archiving"
+			);
+			git(
+				["commit", "-m", "test"],
+				"Failed to create a backup"
+			);
+			newSnapshot = git(
+				["rev-parse", "--short", "HEAD"],
+				"Failed to retrieve current snapshot information"
+			).output.strip('\n');
+		} else {
+			// Если коммит является посленим в ветке
+			git(
+				["add", "."],
+				"Failed to prepare files for archiving"
+			);
+			git(
+				["commit", "-m", "test"],
+				"Failed to create a backup"
+			);
+			newSnapshot = git(
+				["rev-parse", "--short", "HEAD"],
+				"Failed to retrieve current snapshot information"
+			).output.strip('\n');
+			git(
+				["checkout", currentBranch],
+				"Failed to perform intermediate state switching"
+			);
+			git(
+				["merge", newSnapshot],
+				"Issue with including the commit into the branch " ~ currentBranch
+			);
+		}
+		writeln("Backup was created successfully: ", newSnapshot);
 	}
 
 	void list() {
-		auto result = git(
+		string currentSnapshot = git(
 			["rev-parse", "--short", "HEAD"],
 			"Failed to retrieve current snapshot information"
-		);
+		).output.strip('\n');
 
-		string current = result.output.strip('\n');
+		git(
-
-		result = git(
 			[
 				"log",
 				"--all",
@@ -149,11 +186,8 @@ class Snag {
 				"--pretty=format:%ad\t%h"
 			],
 			"Failed to retrieve the list of snapshots"
-		);
+		).output.split('\n').map!(line => line.split('\t')).array.each!(e =>
-
+			writefln("%s\t%s\t%s", currentSnapshot == e[1] ? "    >" : "", e[0], e[1])
-		result.output.split('\n').map!(line => line.split('\t')).array
-			.sort!((a, b) => a[0] > b[0]).each!(e =>
-			writefln("%s\t%s\t%s", current == e[1] ? "    >" : "", e[0], e[1])
 		);
 	}
 
@@ -182,6 +216,6 @@ class Snag {
 			["checkout", hash],
 			"Failed to restore the snapshot state " ~ hash
 		);
-		writeln("Backup was restored successfully");
+		writeln("Backup was restored successfully: ", hash);
 	}
 }