diff --git a/.pylintrc b/.pylintrc
index c6dcdc0..b5c747f 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -430,7 +430,8 @@ disable=raw-checker-failed,
         deprecated-pragma,
         use-symbolic-message-instead,
         use-implicit-booleaness-not-comparison-to-string,
-        use-implicit-booleaness-not-comparison-to-zero
+        use-implicit-booleaness-not-comparison-to-zero,
+        unspecified-encoding
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
diff --git a/.vscode/launch.json b/.vscode/launch.json
index 99814f0..caf4bfc 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -6,7 +6,7 @@
   "configurations": [
     {
       "name": "Launch ESBMC-AI on Open File",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "module": "esbmc_ai",
       "justMyCode": true,
@@ -17,7 +17,7 @@
     },
     {
       "name": "Fix Code on Open File",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "module": "esbmc_ai",
       "justMyCode": true,
@@ -31,7 +31,7 @@
     },
     {
       "name": "Optimize Code on Open File",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "module": "esbmc_ai",
       "justMyCode": true,
@@ -44,7 +44,7 @@
     },
     {
       "name": "Python: Current File",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "program": "${file}",
       "console": "integratedTerminal",
@@ -52,7 +52,7 @@
     },
     {
       "name": "Run tests",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "module": "pytest",
       "justMyCode": true,
@@ -63,7 +63,7 @@
     },
     {
       "name": "Run coverage tests",
-      "type": "python",
+      "type": "debugpy",
       "request": "launch",
       "module": "pytest",
       "justMyCode": true,
diff --git a/Pipfile b/Pipfile
index c739635..3f3c2e2 100644
--- a/Pipfile
+++ b/Pipfile
@@ -25,6 +25,7 @@ clang = "*"
 langchain = "*"
 langchain-openai = "*"
 langchain-community = "*"
+lizard = "*"
 
 [dev-packages]
 pylint = "*"
diff --git a/config.json b/config.json
index 06a4f43..dd1f40a 100644
--- a/config.json
+++ b/config.json
@@ -70,7 +70,7 @@
       ]
     },
     "generate_solution": {
-      "max_attempts": 4,
+      "max_attempts": 5,
       "temperature": 0.0,
       "message_history": "normal",
       "scenarios": {
@@ -87,8 +87,13 @@
           ]
         }
       },
-      "system": [],
-      "initial": "From now on, act as an Automated Code Repair Tool that repairs AI C code. You will be shown AI C code, along with ESBMC output. Pay close attention to the ESBMC output, which contains a stack trace along with the type of error that occurred and its location. Provide the repaired C code as output, as would an Automated Code Repair Tool. Aside from the corrected source code, do not output any other text. The ESBMC output is {esbmc_output} The source code is {source_code}"
+      "system": [
+        {
+          "role": "System",
+          "content": "From now on, act as an Automated Code Repair Tool that repairs AI C code. You will be shown AI C code, along with ESBMC output. Pay close attention to the ESBMC output, which contains a stack trace along with the type of error that occurred and its location. "
+        }
+      ],
+      "initial": "Provide the repaired C code as output, as would an Automated Code Repair Tool. Aside from the corrected source code, do not output any other text. The ESBMC output is {esbmc_output} The source code is {source_code}"
     }
   }
 }
\ No newline at end of file
diff --git a/esbmc_ai/__main__.py b/esbmc_ai/__main__.py
index 8c528d3..e9a715d 100755
--- a/esbmc_ai/__main__.py
+++ b/esbmc_ai/__main__.py
@@ -3,11 +3,17 @@
 # Author: Yiannis Charalambous 2023
 
 import os
+from pathlib import Path
 import re
 import sys
 
 # Enables arrow key functionality for input(). Do not remove import.
 import readline
+from typing import Optional
+
+from esbmc_ai.commands.fix_code_command import FixCodeCommandResult
+
+_ = readline
 
 import argparse
 from langchain.base_language import BaseLanguageModel
@@ -15,12 +21,7 @@
 
 import esbmc_ai.config as config
 from esbmc_ai import __author__, __version__
-from esbmc_ai.frontend.solution import (
-    SourceFile,
-    get_main_source_file,
-    set_main_source_file,
-    get_main_source_file_path,
-)
+from esbmc_ai.solution import SourceFile, Solution, get_solution
 
 from esbmc_ai.commands import (
     ChatCommand,
@@ -30,7 +31,7 @@
 )
 
 from esbmc_ai.loading_widget import LoadingWidget, create_loading_widget
-from esbmc_ai.user_chat import UserChat
+from esbmc_ai.chats import UserChat
 from esbmc_ai.logging import print_horizontal_line, printv, printvv
 from esbmc_ai.esbmc_util import esbmc
 from esbmc_ai.chat_response import FinishReason, ChatResponse
@@ -123,7 +124,34 @@ def init_commands_list() -> None:
 
 
 def update_solution(source_code: str) -> None:
-    set_main_source_file(SourceFile(get_main_source_file_path(), source_code))
+    get_solution().files[0].update_content(content=source_code, reset_changes=True)
+
+
+def _run_esbmc(source_file: SourceFile, anim: Optional[LoadingWidget] = None) -> str:
+    assert source_file.file_path
+
+    if anim:
+        anim.start("ESBMC is processing... Please Wait")
+    exit_code, esbmc_output = esbmc(
+        path=source_file.file_path,
+        esbmc_params=config.esbmc_params,
+        timeout=config.verifier_timeout,
+    )
+    if anim:
+        anim.stop()
+
+    # ESBMC will output 0 for verification success and 1 for verification
+    # failed, if anything else gets thrown, it's an ESBMC error.
+    if not config.allow_successful and exit_code == 0:
+        printv("Success!")
+        print(esbmc_output)
+        sys.exit(0)
+    elif exit_code != 0 and exit_code != 1:
+        printv(f"ESBMC exit code: {exit_code}")
+        printv(f"ESBMC Output:\n\n{esbmc_output}")
+        sys.exit(1)
+
+    return esbmc_output
 
 
 def init_commands() -> None:
@@ -137,25 +165,30 @@ def init_commands() -> None:
     fix_code_command.on_solution_signal.add_listener(update_solution)
 
 
-def _run_command_mode(
-    command: ChatCommand,
-    args: list[str],
-    esbmc_output: str,
-    source_code: str,
-) -> None:
+def _run_command_mode(command: ChatCommand, args: argparse.Namespace) -> None:
+    path_arg: Path = Path(args.filename)
+
+    solution: Solution = get_solution()
+    if path_arg.is_dir():
+        for path in path_arg.glob("**/*"):
+            if path.is_file() and path.name:
+                solution.add_source_file(path, None)
+    else:
+        solution.add_source_file(path_arg, None)
+
     match command.command_name:
         case fix_code_command.command_name:
-            error, solution = fix_code_command.execute(
-                file_name=get_main_source_file_path(),
-                source_code=source_code,
-                esbmc_output=esbmc_output,
-            )
-
-            if error:
-                print("Failed all attempts...")
-                sys.exit(1)
-            else:
-                print(solution)
+            for source_file in solution.files:
+                # Run ESBMC first round
+                esbmc_output: str = _run_esbmc(source_file)
+                source_file.assign_verifier_output(esbmc_output)
+
+                result: FixCodeCommandResult = fix_code_command.execute(
+                    source_file=source_file,
+                    generate_patches=config.generate_patches,
+                )
+
+                print(result)
         case _:
             command.execute()
     sys.exit(0)
@@ -249,7 +282,15 @@ def main() -> None:
         + "}",
     )
 
-    args = parser.parse_args()
+    parser.add_argument(
+        "-p",
+        "--generate-patches",
+        action="store_true",
+        default=False,
+        help="Generate patch files and place them in the same folder as the source files.",
+    )
+
+    args: argparse.Namespace = parser.parse_args()
 
     print(f"ESBMC-AI {__version__}")
     print(f"Made by {__author__}")
@@ -270,39 +311,12 @@ def main() -> None:
     printv("Reading source code...")
     print(f"Running ESBMC with {config.esbmc_params}\n")
 
-    # Cast to string (for language servers)
-    args.filename = str(args.filename)
-
-    # Read source code
-    with open(args.filename, mode="r") as file:
-        # Add the main source file to the solution explorer.
-        set_main_source_file(SourceFile(args.filename, file.read()))
+    assert isinstance(args.filename, str)
 
-    anim.start("ESBMC is processing... Please Wait")
-    exit_code, esbmc_output = esbmc(
-        path=get_main_source_file_path(),
-        esbmc_params=config.esbmc_params,
-        timeout=config.verifier_timeout,
-    )
-    anim.stop()
-
-    # Print verbose lvl 2
-    print_horizontal_line(2)
-    printvv(esbmc_output)
-    print_horizontal_line(2)
-
-    # ESBMC will output 0 for verification success and 1 for verification
-    # failed, if anything else gets thrown, it's an ESBMC error.
-    if not config.allow_successful and exit_code == 0:
-        print("Success!")
-        print(esbmc_output)
-        sys.exit(0)
-    elif exit_code != 0 and exit_code != 1:
-        print(f"ESBMC exit code: {exit_code}")
-        print(f"ESBMC Output:\n\n{esbmc_output}")
-        sys.exit(1)
-
-    # Command mode: Check if command is called and call it.
+    # ===========================================
+    # Command mode
+    # ===========================================
+    # Check if command is called and call it.
     # If not, then continue to user mode.
     if args.command != None:
         command = args.command
@@ -310,14 +324,46 @@ def main() -> None:
             print("Running Command:", command)
             for idx, command_name in enumerate(command_names):
                 if command == command_name:
-                    _run_command_mode(
-                        command=commands[idx],
-                        args=[],  # NOTE: Currently not supported...
-                        source_code=get_main_source_file().content,
-                        esbmc_output=esbmc_output,
-                    )
+                    _run_command_mode(command=commands[idx], args=args)
             sys.exit(0)
 
+    # ===========================================
+    # User Mode (Supports only 1 file)
+    # ===========================================
+
+    # Init Solution
+    solution: Solution
+    # Determine if we are processing one file versus multiple files
+    path_arg: Path = Path(args.filename)
+    if path_arg.is_dir():
+        # Load only files.
+        print(
+            "Processing multiple files is not supported in User Mode."
+            "Call a command using -c to process directories"
+        )
+        sys.exit(1)
+    else:
+        # Add the main source file to the solution explorer.
+        solution: Solution = get_solution()
+        solution.add_source_file(path_arg, None)
+    del path_arg
+
+    # Assert that we have one file and one filepath
+    assert len(solution.files) == 1
+
+    source_file: SourceFile = solution.files[0]
+    assert source_file.file_path
+
+    esbmc_output: str = _run_esbmc(source_file, anim)
+
+    # Print verbose lvl 2
+    print_horizontal_line(2)
+    printvv(esbmc_output)
+    print_horizontal_line(2)
+
+    source_file.assign_verifier_output(esbmc_output)
+    del esbmc_output
+
     printv(f"Initializing the LLM: {config.ai_model.name}\n")
     chat_llm: BaseLanguageModel = config.ai_model.create_llm(
         api_keys=config.api_keys,
@@ -332,8 +378,8 @@ def main() -> None:
         ai_model_agent=config.chat_prompt_user_mode,
         ai_model=config.ai_model,
         llm=chat_llm,
-        source_code=get_main_source_file().content,
-        esbmc_output=esbmc_output,
+        source_code=source_file.latest_content,
+        esbmc_output=source_file.latest_verifier_output,
         set_solution_messages=config.chat_prompt_user_mode.scenarios["set_solution"],
     )
 
@@ -345,7 +391,6 @@ def main() -> None:
     if len(config.chat_prompt_user_mode.initial_prompt) > 0:
         printv("Using initial prompt from file...\n")
         anim.start("Model is parsing ESBMC output... Please Wait")
-        # TODO Make protected
         response = chat.send_message(
             message=config.chat_prompt_user_mode.initial_prompt,
         )
@@ -375,17 +420,16 @@ def main() -> None:
                 print()
                 print("ESBMC-AI will generate a fix for the code...")
 
-                error, solution = fix_code_command.execute(
-                    file_name=get_main_source_file_path(),
-                    source_code=get_main_source_file().content,
-                    esbmc_output=esbmc_output,
+                result: FixCodeCommandResult = fix_code_command.execute(
+                    source_file=source_file,
+                    generate_patches=config.generate_patches,
                 )
 
-                if not error:
+                if result.successful:
                     print(
                         "\n\nESBMC-AI: Here is the corrected code, verified with ESBMC:"
                     )
-                    print(f"```\n{solution}\n```")
+                    print(f"```\n{result.repaired_source}\n```")
                 continue
             else:
                 # Commands without parameters or returns are handled automatically.
diff --git a/esbmc_ai/chats/__init__.py b/esbmc_ai/chats/__init__.py
new file mode 100644
index 0000000..e2b4c2a
--- /dev/null
+++ b/esbmc_ai/chats/__init__.py
@@ -0,0 +1,13 @@
+# Author: Yiannis Charalambous
+
+from .base_chat_interface import BaseChatInterface
+from .latest_state_solution_generator import LatestStateSolutionGenerator
+from .solution_generator import SolutionGenerator
+from .user_chat import UserChat
+
+__all__ = [
+    "BaseChatInterface",
+    "LatestStateSolutionGenerator",
+    "SolutionGenerator",
+    "UserChat",
+]
diff --git a/esbmc_ai/base_chat_interface.py b/esbmc_ai/chats/base_chat_interface.py
similarity index 97%
rename from esbmc_ai/base_chat_interface.py
rename to esbmc_ai/chats/base_chat_interface.py
index e6fc41f..6344734 100644
--- a/esbmc_ai/base_chat_interface.py
+++ b/esbmc_ai/chats/base_chat_interface.py
@@ -13,8 +13,8 @@
 )
 
 from esbmc_ai.config import ChatPromptSettings
-from .chat_response import ChatResponse, FinishReason
-from .ai_models import AIModel
+from esbmc_ai.chat_response import ChatResponse, FinishReason
+from esbmc_ai.ai_models import AIModel
 
 
 class BaseChatInterface(object):
diff --git a/esbmc_ai/latest_state_solution_generator.py b/esbmc_ai/chats/latest_state_solution_generator.py
similarity index 93%
rename from esbmc_ai/latest_state_solution_generator.py
rename to esbmc_ai/chats/latest_state_solution_generator.py
index 81d15a5..0bda6f8 100644
--- a/esbmc_ai/latest_state_solution_generator.py
+++ b/esbmc_ai/chats/latest_state_solution_generator.py
@@ -2,7 +2,7 @@
 
 from typing_extensions import override
 from langchain_core.messages import BaseMessage
-from esbmc_ai.solution_generator import SolutionGenerator
+from esbmc_ai.chats.solution_generator import SolutionGenerator
 from esbmc_ai.chat_response import FinishReason
 
 # TODO Test me
diff --git a/esbmc_ai/solution_generator.py b/esbmc_ai/chats/solution_generator.py
similarity index 97%
rename from esbmc_ai/solution_generator.py
rename to esbmc_ai/chats/solution_generator.py
index 95b8eec..6187ee3 100644
--- a/esbmc_ai/solution_generator.py
+++ b/esbmc_ai/chats/solution_generator.py
@@ -8,9 +8,9 @@
 
 from esbmc_ai.chat_response import ChatResponse, FinishReason
 from esbmc_ai.config import ChatPromptSettings, DynamicAIModelAgent
-from esbmc_ai.frontend.solution import apply_line_patch
+from esbmc_ai.solution import SourceFile
 
-from .ai_models import AIModel
+from esbmc_ai.ai_models import AIModel
 from .base_chat_interface import BaseChatInterface
 from esbmc_ai.esbmc_util import (
     esbmc_get_counter_example,
@@ -205,6 +205,8 @@ def generate_solution(self) -> tuple[str, FinishReason]:
                 assert (
                     line
                 ), "fix code command: error line could not be found to apply brutal patch replacement"
-                solution = apply_line_patch(self.source_code_raw, solution, line, line)
+                solution = SourceFile.apply_line_patch(
+                    self.source_code_raw, solution, line, line
+                )
 
         return solution, response.finish_reason
diff --git a/esbmc_ai/user_chat.py b/esbmc_ai/chats/user_chat.py
similarity index 98%
rename from esbmc_ai/user_chat.py
rename to esbmc_ai/chats/user_chat.py
index 0e1bbfd..3c1cdd6 100644
--- a/esbmc_ai/user_chat.py
+++ b/esbmc_ai/chats/user_chat.py
@@ -9,8 +9,8 @@
 from langchain.schema import BaseMessage, SystemMessage
 
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
+from esbmc_ai.ai_models import AIModel
 
-from .ai_models import AIModel
 from .base_chat_interface import BaseChatInterface
 
 
diff --git a/esbmc_ai/commands/chat_command.py b/esbmc_ai/commands/chat_command.py
index c91105e..6109e1c 100644
--- a/esbmc_ai/commands/chat_command.py
+++ b/esbmc_ai/commands/chat_command.py
@@ -3,6 +3,8 @@
 from abc import ABC, abstractmethod
 from typing import Any, Optional
 
+from esbmc_ai.commands.command_result import CommandResult
+
 
 class ChatCommand(ABC):
     command_name: str
@@ -17,7 +19,6 @@ def __init__(
         self.command_name = command_name
         self.help_message = help_message
 
-
     @abstractmethod
-    def execute(self, **kwargs: Optional[Any]) -> Optional[Any]:
+    def execute(self, **kwargs: Optional[Any]) -> Optional[CommandResult]:
         raise NotImplementedError(f"Command {self.command_name} is not implemented.")
diff --git a/esbmc_ai/commands/command_result.py b/esbmc_ai/commands/command_result.py
new file mode 100644
index 0000000..58703cc
--- /dev/null
+++ b/esbmc_ai/commands/command_result.py
@@ -0,0 +1,15 @@
+# Author: Yiannis Charalambous
+
+from abc import abstractmethod
+
+
+class CommandResult:
+    @property
+    @abstractmethod
+    def successful(self) -> bool:
+        raise NotImplementedError()
+
+    def __str__(self) -> str:
+        return f"Command returned " + (
+            "successful" if self.successful else "unsuccessful"
+        )
diff --git a/esbmc_ai/commands/exit_command.py b/esbmc_ai/commands/exit_command.py
index 2fb38dd..943c446 100644
--- a/esbmc_ai/commands/exit_command.py
+++ b/esbmc_ai/commands/exit_command.py
@@ -15,6 +15,6 @@ def __init__(self) -> None:
         )
 
     @override
-    def execute(self, **_: Optional[Any]) -> Optional[Any]:
+    def execute(self, **_: Optional[Any]) -> None:
         print("exiting...")
         sys.exit(0)
diff --git a/esbmc_ai/commands/fix_code_command.py b/esbmc_ai/commands/fix_code_command.py
index 97abcab..dce3e2b 100644
--- a/esbmc_ai/commands/fix_code_command.py
+++ b/esbmc_ai/commands/fix_code_command.py
@@ -1,12 +1,15 @@
 # Author: Yiannis Charalambous
 
 import sys
-from typing import Any, Tuple
+from typing import Any, Optional, Tuple
 from typing_extensions import override
 
 from esbmc_ai.chat_response import FinishReason
-from esbmc_ai.latest_state_solution_generator import LatestStateSolutionGenerator
+from esbmc_ai.chats import LatestStateSolutionGenerator, SolutionGenerator
+from esbmc_ai.chats.solution_generator import ESBMCTimedOutException
+from esbmc_ai.commands.command_result import CommandResult
 from esbmc_ai.reverse_order_solution_generator import ReverseOrderSolutionGenerator
+from esbmc_ai.solution import SourceFile
 
 from .chat_command import ChatCommand
 from .. import config
@@ -16,11 +19,28 @@
     esbmc_get_error_type,
     esbmc_load_source_code,
 )
-from ..solution_generator import (
-    ESBMCTimedOutException,
-    SolutionGenerator,
-)
 from ..logging import print_horizontal_line, printv, printvv
+from subprocess import CalledProcessError
+
+
+class FixCodeCommandResult(CommandResult):
+    def __init__(self, successful: bool, repaired_source: Optional[str] = None) -> None:
+        super().__init__()
+        self._successful: bool = successful
+        self.repaired_source: Optional[str] = repaired_source
+
+    @property
+    @override
+    def successful(self) -> bool:
+        return self._successful
+
+    @override
+    def __str__(self) -> str:
+        return (
+            self.repaired_source
+            if self._successful and self.repaired_source != None
+            else "ESBMC-AI Notice: Failed all attempts..."
+        )
 
 
 class FixCodeCommand(ChatCommand):
@@ -34,7 +54,7 @@ def __init__(self) -> None:
         self.anim = create_loading_widget()
 
     @override
-    def execute(self, **kwargs: Any) -> Tuple[bool, str]:
+    def execute(self, **kwargs: Any) -> FixCodeCommandResult:
         def print_raw_conversation() -> None:
             print_horizontal_line(0)
             print("ESBMC-AI Notice: Printing raw conversation...")
@@ -44,12 +64,14 @@ def print_raw_conversation() -> None:
             print("\n" + "\n\n".join(messages))
             print("ESBMC-AI Notice: End of raw conversation")
 
-        file_name: str = kwargs["file_name"]
-        source_code: str = kwargs["source_code"]
-        esbmc_output: str = kwargs["esbmc_output"]
+        source_file: SourceFile = kwargs["source_file"]
+        assert source_file.file_path
+        generate_patches: bool = (
+            kwargs["generate_patches"] if "generate_patches" in kwargs else False
+        )
 
         # Parse the esbmc output here and determine what "Scenario" to use.
-        scenario: str = esbmc_get_error_type(esbmc_output)
+        scenario: str = esbmc_get_error_type(source_file.initial_verifier_output)
 
         printv(f"Scenario: {scenario}")
         printv(
@@ -108,8 +130,8 @@ def print_raw_conversation() -> None:
 
         try:
             solution_generator.update_state(
-                source_code=source_code,
-                esbmc_output=esbmc_output,
+                source_code=source_file.latest_content,
+                esbmc_output=source_file.latest_verifier_output,
             )
         except ESBMCTimedOutException:
             print("error: ESBMC has timed out...")
@@ -117,8 +139,8 @@ def print_raw_conversation() -> None:
 
         print()
 
-        max_retries: int = config.fix_code_max_attempts
-        for idx in range(max_retries):
+        attempts: int = config.fix_code_max_attempts
+        for attempt in range(1, attempts + 1):
             # Get a response. Use while loop to account for if the message stack
             # gets full, then need to compress and retry.
             while True:
@@ -129,13 +151,13 @@ def print_raw_conversation() -> None:
                 if finish_reason == FinishReason.length:
                     solution_generator.compress_message_stack()
                 else:
-                    source_code = llm_solution
+                    source_file.update_content(llm_solution)
                     break
 
             # Print verbose lvl 2
             printvv("\nESBMC-AI Notice: Source Code Generation:")
             print_horizontal_line(2)
-            printvv(source_code)
+            printvv(source_file.latest_content)
             print_horizontal_line(2)
             printvv("")
 
@@ -143,34 +165,45 @@ def print_raw_conversation() -> None:
             # to a temporary location since ESBMC needs it in file format.
             self.anim.start("Verifying with ESBMC... Please Wait")
             exit_code, esbmc_output = esbmc_load_source_code(
-                file_path=file_name,
-                source_code=source_code,
+                source_file=source_file,
+                source_file_content_index=-1,
                 esbmc_params=config.esbmc_params,
                 auto_clean=config.temp_auto_clean,
                 timeout=config.verifier_timeout,
             )
             self.anim.stop()
 
+            source_file.assign_verifier_output(esbmc_output)
+            del esbmc_output
+
             # Print verbose lvl 2
             printvv("\nESBMC-AI Notice: ESBMC Output:")
             print_horizontal_line(2)
-            printvv(esbmc_output)
+            printvv(source_file.latest_verifier_output)
             print_horizontal_line(2)
 
             # Solution found
             if exit_code == 0:
-                self.on_solution_signal.emit(source_code)
+                self.on_solution_signal.emit(source_file.latest_content)
 
                 if config.raw_conversation:
                     print_raw_conversation()
 
                 printv("ESBMC-AI Notice: Successfully verified code")
 
-                return False, source_code
+                returned_source: str
+                if generate_patches:
+                    returned_source = source_file.get_patch(0, -1)
+                else:
+                    returned_source = source_file.latest_content
+
+                return FixCodeCommandResult(True, returned_source)
 
             try:
                 # Update state
-                solution_generator.update_state(source_code, esbmc_output)
+                solution_generator.update_state(
+                    source_file.latest_content, source_file.latest_verifier_output
+                )
             except ESBMCTimedOutException:
                 if config.raw_conversation:
                     print_raw_conversation()
@@ -178,13 +211,12 @@ def print_raw_conversation() -> None:
                 sys.exit(1)
 
             # Failure case
-            print(
-                f"ESBMC-AI Notice: Failure {idx+1}/{max_retries}" + ": Retrying..."
-                if idx != max_retries - 1
-                else ""
-            )
+            if attempt != attempts:
+                print(f"ESBMC-AI Notice: Failure {attempt}/{attempts}: Retrying...")
+            else:
+                print(f"ESBMC-AI Notice: Failure {attempt}/{attempts}")
 
         if config.raw_conversation:
             print_raw_conversation()
 
-        return True, "ESBMC-AI Notice: Failed all attempts..."
+        return FixCodeCommandResult(False, None)
diff --git a/esbmc_ai/config.py b/esbmc_ai/config.py
index 44007b3..28b4ccc 100644
--- a/esbmc_ai/config.py
+++ b/esbmc_ai/config.py
@@ -37,7 +37,7 @@
 ]
 
 temp_auto_clean: bool = True
-temp_file_dir: str = "."
+temp_file_dir: Optional[str] = None
 ai_model: AIModel
 
 esbmc_output_type: str = "full"
@@ -57,6 +57,8 @@
 
 cfg_path: str
 
+generate_patches: bool
+
 
 # TODO Get rid of this class as soon as ConfigTool with the pyautoconfig
 class AIAgentConversation(NamedTuple):
@@ -498,3 +500,6 @@ def load_args(args) -> None:
         esbmc_params.extend(args.remaining)
     elif len(args.remaining) != 0:
         esbmc_params = args.remaining
+
+    global generate_patches
+    generate_patches = args.generate_patches
diff --git a/esbmc_ai/esbmc_util.py b/esbmc_ai/esbmc_util.py
index 4a12013..a034a2e 100644
--- a/esbmc_ai/esbmc_util.py
+++ b/esbmc_ai/esbmc_util.py
@@ -6,6 +6,8 @@
 from pathlib import Path
 from typing import Optional
 
+from esbmc_ai.solution import SourceFile
+
 from . import config
 
 
@@ -91,13 +93,13 @@ def get_clang_err_line_index(clang_output: str) -> Optional[int]:
         return None
 
 
-def esbmc(path: str, esbmc_params: list, timeout: Optional[float] = None):
+def esbmc(path: Path, esbmc_params: list, timeout: Optional[float] = None):
     """Exit code will be 0 if verification successful, 1 if verification
     failed. And any other number for compilation error/general errors."""
     # Build parameters
     esbmc_cmd = [config.esbmc_path]
     esbmc_cmd.extend(esbmc_params)
-    esbmc_cmd.append(path)
+    esbmc_cmd.append(str(path))
 
     if "--timeout" in esbmc_cmd:
         print(
@@ -123,38 +125,34 @@ def esbmc(path: str, esbmc_params: list, timeout: Optional[float] = None):
 
 
 def esbmc_load_source_code(
-    file_path: str,
-    source_code: str,
+    source_file: SourceFile,
+    source_file_content_index: int,
     esbmc_params: list = config.esbmc_params,
     auto_clean: bool = config.temp_auto_clean,
     timeout: Optional[float] = None,
 ):
-    source_code_path = Path(file_path)
-
-    # Create temp path.
-    delete_path: bool = False
-    if not os.path.exists(config.temp_file_dir):
-        os.mkdir(config.temp_file_dir)
-        delete_path = True
-
-    temp_file_path = f"{config.temp_file_dir}{os.sep}{source_code_path.name}"
 
-    # Create temp file.
-    with open(temp_file_path, "w") as file:
-        # Save to temporary folder and flush contents.
-        file.write(source_code)
-        file.flush()
+    file_path: Path
+    if config.temp_file_dir:
+        file_path = source_file.save_file(
+            file_path=Path(config.temp_file_dir),
+            temp_dir=False,
+            index=source_file_content_index,
+        )
+    else:
+        file_path = source_file.save_file(
+            file_path=None,
+            temp_dir=True,
+            index=source_file_content_index,
+        )
 
-        # Call ESBMC to temporary folder.
-        results = esbmc(file.name, esbmc_params, timeout=timeout)
+    # Call ESBMC to temporary folder.
+    results = esbmc(file_path, esbmc_params, timeout=timeout)
 
     # Delete temp files and path
     if auto_clean:
         # Remove file
-        os.remove(temp_file_path)
-        # Remove file path if created this run and is empty.
-        if delete_path and len(os.listdir(config.temp_file_dir)) == 0:
-            os.rmdir(config.temp_file_dir)
+        os.remove(file_path)
 
     # Return
     return results
diff --git a/esbmc_ai/frontend/__init__.py b/esbmc_ai/frontend/__init__.py
deleted file mode 100644
index 1f91aa3..0000000
--- a/esbmc_ai/frontend/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-# Author: Yiannis Charalambous
diff --git a/esbmc_ai/frontend/solution.py b/esbmc_ai/frontend/solution.py
deleted file mode 100644
index 3437ddf..0000000
--- a/esbmc_ai/frontend/solution.py
+++ /dev/null
@@ -1,61 +0,0 @@
-# Author: Yiannis Charalambous
-
-"""# Solution
-Keeps track of all the source files that ESBMC-AI is targeting."""
-
-from typing import NamedTuple
-
-
-class SourceFile(NamedTuple):
-    file_path: str
-    content: str
-
-
-_main_source_file: SourceFile = SourceFile("", "")
-_source_files: set[SourceFile] = set()
-
-
-def add_source_file(source_file: SourceFile) -> None:
-    global _source_files
-    _source_files.add(source_file)
-
-
-def set_main_source_file(source_file: SourceFile) -> None:
-    add_source_file(source_file)
-    global _main_source_file
-    _main_source_file = source_file
-
-
-def get_main_source_file_path() -> str:
-    global _main_source_file
-    return _main_source_file.file_path
-
-
-def get_main_source_file() -> SourceFile:
-    global _main_source_file
-    return _main_source_file
-
-
-def get_source_files() -> list[SourceFile]:
-    global _source_files
-    return list(_source_files)
-
-
-def apply_line_patch(source_code: str, patch: str, start: int, end: int) -> str:
-    """Applies a patch to the source code.
-
-    To replace a single line, start and end are equal.
-
-    Args:
-        * source_code - The source code to apply the patch to.
-        * patch - Can be a line or multiple lines but will replace the start and
-        end region defined.
-        * start - Line index to mark start of replacement.
-        * end - Marks the end of the region where the patch will be applied to.
-        End is non-inclusive."""
-    assert (
-        start <= end
-    ), f"start ({start}) needs to be less than or equal to end ({end})"
-    lines: list[str] = source_code.splitlines()
-    lines = lines[:start] + [patch] + lines[end + 1 :]
-    return "\n".join(lines)
diff --git a/esbmc_ai/optimize_code.py b/esbmc_ai/optimize_code.py
deleted file mode 100644
index 092c2ce..0000000
--- a/esbmc_ai/optimize_code.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# Author: Yiannis Charalambous
-
-from langchain.base_language import BaseLanguageModel
-from langchain.schema import AIMessage, BaseMessage, HumanMessage
-
-from esbmc_ai.config import ChatPromptSettings
-from .base_chat_interface import BaseChatInterface, ChatResponse
-from .ai_models import AIModel
-
-
-class OptimizeCode(BaseChatInterface):
-    initial_message: str
-
-    def __init__(
-        self,
-        ai_model_agent: ChatPromptSettings,
-        initial_message: str,
-        ai_model: AIModel,
-        llm: BaseLanguageModel,
-    ) -> None:
-        super().__init__(ai_model_agent=ai_model_agent, ai_model=ai_model, llm=llm)
-
-        self.initial_message = initial_message
-
-    def optimize_function(self, source_code: str, function_name: str) -> ChatResponse:
-        self.messages = []
-        self.push_to_message_stack(
-            HumanMessage(
-                content=f"Reply OK if you understand the following is the source code to optimize:\n\n{source_code}"
-            )
-        )
-        self.push_to_message_stack(AIMessage(content="OK."))
-
-        expanded_initial_message: str = self.initial_message.replace(
-            "%s", function_name
-        )
-        return self.send_message(expanded_initial_message)
diff --git a/esbmc_ai/reverse_order_solution_generator.py b/esbmc_ai/reverse_order_solution_generator.py
index bd13d46..203b2ea 100644
--- a/esbmc_ai/reverse_order_solution_generator.py
+++ b/esbmc_ai/reverse_order_solution_generator.py
@@ -2,7 +2,7 @@
 
 from langchain.schema import BaseMessage
 from typing_extensions import override, Optional
-from esbmc_ai.solution_generator import SolutionGenerator
+from esbmc_ai.chats.solution_generator import SolutionGenerator
 from esbmc_ai.chat_response import ChatResponse
 
 # TODO Test me
diff --git a/esbmc_ai/solution.py b/esbmc_ai/solution.py
new file mode 100644
index 0000000..05cf2a2
--- /dev/null
+++ b/esbmc_ai/solution.py
@@ -0,0 +1,276 @@
+# Author: Yiannis Charalambous
+
+"""# Solution
+Keeps track of all the source files that ESBMC-AI is targeting. """
+
+import os
+from typing import Optional
+from pathlib import Path
+from subprocess import PIPE, STDOUT, run, CompletedProcess
+from tempfile import NamedTemporaryFile, gettempdir
+import lizard
+
+
+class SourceFile:
+    """Represents a source file in the Solution. This class also holds the
+    verifier output. Contains methods to manipulate and get information about
+    different versions."""
+
+    @classmethod
+    def apply_line_patch(
+        cls, source_code: str, patch: str, start: int, end: int
+    ) -> str:
+        """Applies a patch to the source code.
+
+        To replace a single line, start and end are equal.
+
+        Args:
+            * source_code - The source code to apply the patch to.
+            * patch - Can be a line or multiple lines but will replace the start and
+            end region defined.
+            * start - Line index to mark start of replacement.
+            * end - Marks the end of the region where the patch will be applied to.
+            End is non-inclusive."""
+        assert (
+            start <= end
+        ), f"start ({start}) needs to be less than or equal to end ({end})"
+        lines: list[str] = source_code.splitlines()
+        lines = lines[:start] + [patch] + lines[end + 1 :]
+        return "\n".join(lines)
+
+    def __init__(
+        self, file_path: Optional[Path], content: str, file_ext: Optional[str] = None
+    ) -> None:
+        self._file_path: Optional[Path] = file_path
+        # Content file shows the file throughout the repair process. Index 0 is
+        # the orignial.
+        self._content: list[str] = [content]
+        # Map _content (each iteration) to esbmc output
+        self._esbmc_output: dict[int, str] = {}
+        self._file_ext: Optional[str] = file_ext
+
+    @property
+    def file_path(self) -> Optional[Path]:
+        """Returns the file path of this source file."""
+        return self._file_path
+
+    @property
+    def file_extension(self) -> str:
+        if self._file_ext:
+            return self._file_ext
+        elif self._file_path:
+            return self._file_path.suffix
+        else:
+            raise ValueError("No extension for SourceFile could be resolved")
+
+    @property
+    def initial_content(self) -> str:
+        """Returns the initial state content."""
+        return self._content[0]
+
+    @property
+    def latest_content(self) -> str:
+        """Returns the latest available content."""
+        return self._content[-1]
+
+    @property
+    def content(self) -> tuple[str, ...]:
+        """Returns a tuple of the content of this source file."""
+        return tuple(self._content)
+
+    @property
+    def initial_verifier_output(self) -> str:
+        """Returns the first verifier output"""
+        assert 0 in self._esbmc_output, "Error: No initial verifier output assigned."
+        return self._esbmc_output[0]
+
+    @property
+    def latest_verifier_output(self) -> str:
+        """Returns the latest verifier output"""
+        return self._esbmc_output[len(self._content) - 1]
+
+    @property
+    def verifier_output(self) -> dict[int, str]:
+        """Returns the verifier outputs of the SourceFile"""
+        return self._esbmc_output
+
+    def get_patch(self, index_a: int, index_b: int) -> str:
+        """Return diff between `index_a` and `index_b` which are indicies
+        referencing the content list."""
+        assert len(self._content) > index_a and len(self._content) > index_b
+
+        # Save as temp files
+        with (
+            NamedTemporaryFile(mode="w", delete=False) as file_a,
+            NamedTemporaryFile(mode="w", delete=False) as file_b,
+        ):
+            file_a.write(self._content[index_a])
+            file_a.flush()
+            file_b.write(self._content[index_b])
+            file_b.flush()
+
+            cmd = ["diff", file_a.name, file_b.name]
+            process: CompletedProcess = run(
+                cmd,
+                stdout=PIPE,
+                stderr=STDOUT,
+                check=False,
+            )
+
+            # Exit status is 0 if inputs are the same, 1 if different, 2 if trouble.
+            # https://askubuntu.com/questions/698784/exit-code-of-diff
+            if process.returncode == 2:
+                raise ValueError(
+                    f"Diff for {file_a.name} and {file_b.name} failed (exit 2)."
+                )
+
+            return process.stdout.decode("utf-8")
+
+    # Not used
+    # def push_line_patch(self, patch: str, start: int, end: int) -> str:
+    #     """Calls `apply_line_patch` using the latest source code and then pushes
+    #     the new patch to the content."""
+    #     new_source: str = SourceFile.apply_line_patch(
+    #         source_code=self._content[-1],
+    #         patch=patch,
+    #         start=start,
+    #         end=end,
+    #     )
+    #     self._content.append(new_source)
+    #     return new_source
+
+    def update_content(self, content: str, reset_changes: bool = False) -> None:
+        """Ascociates a new version of the content of source code to a file."""
+        if reset_changes:
+            self._content = [content]
+        else:
+            self._content.append(content)
+
+    def assign_verifier_output(self, verifier_output: str, index: int = -1) -> None:
+        """Assigns verifier output to the ascociated file. If no file is given,
+        then assigns to the latest one."""
+        if index < 0:
+            # Simulate negative indicies like with Lists.
+            index = len(self._content) + index
+        self._esbmc_output[index] = verifier_output
+
+    def save_file(
+        self, file_path: Optional[Path], temp_dir: bool = True, index: int = -1
+    ) -> Path:
+        """Saves the source code file. If file_path is not specified, it
+        will generate an automatic name. If temp_dir is True, it will place
+        the saved file in /tmp and use the file_path file name only."""
+
+        file_name: Optional[str] = None
+        dir_path: Optional[Path] = None
+        if file_path:
+            # If file path is a file, then use the name and directory. If not
+            # then use a temporary name and just store the folder.
+            if file_path.is_file():
+                file_name = file_path.name
+                dir_path = file_path.parent
+            else:
+                dir_path = file_path
+        else:
+            if not self._file_path:
+                raise ValueError(
+                    "Source code file does not have a name or file_path to save to"
+                )
+            # Just store the file and use the temp dir.
+            file_name = self._file_path.name
+
+        if temp_dir:
+            dir_path = Path(gettempdir())
+
+        assert (
+            dir_path
+        ), "dir_path could not be retrieved: file_path or temp_dir need to be set."
+
+        # Create path if it does not exist.
+        if not os.path.exists(dir_path):
+            os.mkdir(dir_path)
+
+        with NamedTemporaryFile(
+            mode="w",
+            buffering=-1,
+            newline=None,
+            suffix=self.file_extension,
+            prefix=file_name,
+            dir=dir_path,
+            delete=False,
+        ) as temp_file:
+            temp_file.write(self.content[index])
+            return Path(temp_file.name)
+
+    @classmethod
+    def calculate_cyclomatic_complexity_delta(
+        cls,
+        source_1: "SourceFile",
+        source_2: "SourceFile",
+        temp_dir: bool = True,
+    ) -> Optional[float]:
+        """Calculates the cyclomatic complexity difference between the two source files."""
+        try:
+            file_1: Path = source_1.save_file(None, temp_dir=temp_dir)
+            file_2: Path = source_2.save_file(None, temp_dir=temp_dir)
+
+            cc1 = lizard.analyze_file(file_1)
+            cc2 = lizard.analyze_file(file_2)
+
+            return cc1.average_cyclomatic_complexity - cc2.average_cyclomatic_complexity
+        except IOError:
+            return None
+
+
+class Solution:
+    """Represents a solution, that is a collection of all the source files that
+    ESBMC-AI will be involved in analyzing."""
+
+    def __init__(self, files: Optional[list[Path]] = None) -> None:
+        files = files if files else []
+        self._files: list[SourceFile] = []
+        for file_path in files:
+            with open(file_path, "r") as file:
+                self._files.append(SourceFile(file_path, file.read()))
+
+    @property
+    def files(self) -> tuple[SourceFile, ...]:
+        """Will return a list of the files. Returns by value."""
+        return tuple(self._files)
+
+    @property
+    def files_mapped(self) -> dict[Path, SourceFile]:
+        """Will return the files mapped to their directory. Returns by value."""
+        return {
+            source_file.file_path: source_file
+            for source_file in self._files
+            if source_file.file_path
+        }
+
+    def add_source_file(
+        self, file_path: Optional[Path], content: Optional[str]
+    ) -> None:
+        """Add a source file to the solution."""
+        if file_path:
+            if content:
+                self._files.append(SourceFile(file_path, content))
+            else:
+                with open(file_path, "r") as file:
+                    self._files.append(SourceFile(file_path, file.read()))
+            return
+
+        if content:
+            self._files.append(SourceFile(file_path, content))
+            return
+
+        raise RuntimeError("file_path and content cannot be both invalid!")
+
+
+# Define a global solution (is not required to be used)
+
+_solution: Solution = Solution()
+
+
+def get_solution() -> Solution:
+    """Returns the global default solution object."""
+    return _solution
diff --git a/scripts/function_equivalence.c b/scripts/function_equivalence.c
deleted file mode 100644
index 16cb943..0000000
--- a/scripts/function_equivalence.c
+++ /dev/null
@@ -1,33 +0,0 @@
-#include <assert.h>
-
-///////////////////////////////////////////
-///////////// OLD /////////////////////////
-///////////////////////////////////////////
-
-$function_old;
-
-///////////////////////////////////////////
-///////////// NEW /////////////////////////
-///////////////////////////////////////////
-
-$function_new;
-
-///////////////////////////////////////////
-///////////// ESBMC MAIN //////////////////
-///////////////////////////////////////////
-
-int main()
-{
-    // Need to dynamically build parameters to supply.
-    $parameters_list;
-
-    // Need to call old and new functions and compare results.
-    $function_call_old;
-
-    $function_call_new;
-
-    // Check whether both functions produce the same output
-    assert($function_assert_old == $function_assert_new);
-
-    return 0;
-}
diff --git a/tests/regtest/test_base_chat_interface.py b/tests/regtest/test_base_chat_interface.py
index f7d3db5..8945f9a 100644
--- a/tests/regtest/test_base_chat_interface.py
+++ b/tests/regtest/test_base_chat_interface.py
@@ -2,12 +2,12 @@
 
 import pytest
 
-from langchain.llms.fake import FakeListLLM
+from langchain_community.llms import FakeListLLM
 from langchain.schema import BaseMessage, HumanMessage, AIMessage, SystemMessage
 
 from esbmc_ai.ai_models import AIModel
 from esbmc_ai.chat_response import ChatResponse
-from esbmc_ai.base_chat_interface import BaseChatInterface
+from esbmc_ai.chats.base_chat_interface import BaseChatInterface
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
 
 
diff --git a/tests/test_base_chat_interface.py b/tests/test_base_chat_interface.py
index 8d79412..42b7b1a 100644
--- a/tests/test_base_chat_interface.py
+++ b/tests/test_base_chat_interface.py
@@ -2,10 +2,10 @@
 
 import pytest
 
-from langchain.llms.fake import FakeListLLM
+from langchain_community.llms import FakeListLLM
 from langchain.schema import AIMessage, BaseMessage, HumanMessage, SystemMessage
 from esbmc_ai.ai_models import AIModel
-from esbmc_ai.base_chat_interface import BaseChatInterface
+from esbmc_ai.chats.base_chat_interface import BaseChatInterface
 from esbmc_ai.chat_response import ChatResponse
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
 
diff --git a/tests/test_latest_state_solution_generator.py b/tests/test_latest_state_solution_generator.py
index 61edf4e..679e2d6 100644
--- a/tests/test_latest_state_solution_generator.py
+++ b/tests/test_latest_state_solution_generator.py
@@ -9,7 +9,7 @@
 from esbmc_ai.ai_models import AIModel
 from esbmc_ai.chat_response import ChatResponse
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
-from esbmc_ai.latest_state_solution_generator import LatestStateSolutionGenerator
+from esbmc_ai.chats.latest_state_solution_generator import LatestStateSolutionGenerator
 
 
 @pytest.fixture(scope="function")
diff --git a/tests/test_solution.py b/tests/test_solution.py
index e303c49..f5d189f 100644
--- a/tests/test_solution.py
+++ b/tests/test_solution.py
@@ -1,13 +1,50 @@
 # Author: Yiannis Charalambous
 
-from esbmc_ai.frontend.solution import apply_line_patch
+import pytest
+from esbmc_ai.solution import Solution, SourceFile
+
+#####################################
+# Solution
+#####################################
+
+
+@pytest.fixture(scope="function")
+def solution() -> Solution:
+    return Solution()
+
+
+def test_add_source_file(solution) -> None:
+    src: str = "int main(int argc, char** argv) {return 0;}"
+    solution.add_source_file(None, src)
+    assert (
+        len(solution.files) == 1
+        and solution.files[0].file_path == None
+        and solution.files[0].latest_content == src
+    )
+    src = '#include <stdio.h> int main(int argc, char** argv) { printf("hello world\n"); return 0;}'
+    solution.add_source_file("Testfile1", src)
+    assert (
+        len(solution.files) == 2
+        and solution.files[1].file_path == "Testfile1"
+        and solution.files[1].latest_content == src
+    )
+    assert (
+        len(solution.files_mapped) == 1
+        and solution.files_mapped["Testfile1"].file_path == "Testfile1"
+        and solution.files_mapped["Testfile1"].initial_content == src
+    )
+
+
+#####################################
+# SourceFile
+#####################################
 
 
 def test_apply_line_patch() -> None:
     text = "\n".join(["a", "b", "c", "d", "e", "f", "g"])
     answer = "\n".join(["a", "b", "1", "g"])
-    assert apply_line_patch(text, "1", 2, 5) == answer
+    assert SourceFile.apply_line_patch(text, "1", 2, 5) == answer
 
     text = "\n".join(["a", "b", "c", "d", "e", "f", "g"])
     answer = "\n".join(["a", "b", "c", "1", "e", "f", "g"])
-    assert apply_line_patch(text, "1", 3, 3) == answer
+    assert SourceFile.apply_line_patch(text, "1", 3, 3) == answer
diff --git a/tests/test_solution_generator.py b/tests/test_solution_generator.py
index be6a209..ff86e7b 100644
--- a/tests/test_solution_generator.py
+++ b/tests/test_solution_generator.py
@@ -6,7 +6,7 @@
 
 from esbmc_ai.ai_models import AIModel
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
-from esbmc_ai.solution_generator import SolutionGenerator
+from esbmc_ai.chats.solution_generator import SolutionGenerator
 
 
 @pytest.fixture(scope="function")
diff --git a/tests/test_user_chat.py b/tests/test_user_chat.py
index 3c2eca1..f0198ca 100644
--- a/tests/test_user_chat.py
+++ b/tests/test_user_chat.py
@@ -2,13 +2,13 @@
 
 import pytest
 
-from langchain.llms.fake import FakeListLLM
+from langchain_community.llms import FakeListLLM
 from langchain.schema import AIMessage, SystemMessage
 
 from esbmc_ai.ai_models import AIModel
 from esbmc_ai.chat_response import ChatResponse, FinishReason
 from esbmc_ai.config import AIAgentConversation, ChatPromptSettings
-from esbmc_ai.user_chat import UserChat
+from esbmc_ai.chats.user_chat import UserChat
 
 
 @pytest.fixture