added source code review to methodology section

Chapters/Methodology.tex

@@ -4,11 +4,14 @@
 
 \label{Methodology}
 
-This chapter describes the methodology used to benchmark peer-to-peer
-mesh VPN implementations. The experimental design prioritizes
-reproducibility at every layer; from dependency management to network
-conditions; enabling independent verification of results and
-facilitating future comparative studies.
+This chapter describes the methodology used to benchmark and analyze
+peer-to-peer mesh VPN implementations. The evaluation combines
+performance benchmarking under controlled network conditions with a
+structured source code analysis of each implementation. The
+benchmarking framework prioritizes reproducibility at every layer;
+from pinned dependencies and declarative system configuration to
+automated test orchestration; enabling independent verification of
+results and facilitating future comparative studies.
 
 \section{Experimental Setup}
 
@@ -277,6 +280,60 @@ confidence intervals, which is appropriate for benchmark data that
 may not follow a normal distribution. The nix-cache test (via hyperfine)
 additionally reports standard deviation.
 
+\section{Source Code Analysis}
+
+To complement the performance benchmarks with architectural
+understanding, a structured source code analysis was conducted for
+all ten VPN implementations. The analysis followed three phases.
+
+\subsection{Repository Collection and LLM-Assisted Overview}
+
+The latest main branch of each VPN's git repository was cloned,
+together with key dependencies that implement core functionality
+outside the main repository. For example, Yggdrasil delegates its
+routing and cryptographic operations to the Ironwood library, which
+was analyzed alongside the main codebase.
+
+Ten LLM agents (Claude Code) were then spawned in parallel, one per
+VPN. Each agent was instructed to read the full source tree and
+produce an \texttt{overview.md} file documenting the following
+aspects:
+
+\begin{itemize}
+  \item Wire protocol and message framing
+  \item Encryption scheme and key exchange
+  \item Packet handling and performance
+  \item NAT traversal mechanism
+  \item Local routing and peer discovery
+  \item Security features and access control
+  \item Resilience / Central Point of Failure
+\end{itemize}
+
+Every claim in the generated overview was required to reference the
+specific file and line range in the repository that supports it,
+enabling direct verification.
+
+\subsection{Manual Verification}
+
+The LLM-generated overviews served as a navigational aid rather than
+a trusted source. The most important code paths identified in each
+overview were manually read and verified against the actual source
+code, correcting inaccuracies and deepening the analysis where the
+automated summaries remained superficial.
+
+\subsection{Feature Matrix and Maintainer Review}
+
+The findings from both the automated and manual analysis were
+consolidated into a comprehensive feature matrix cataloguing 131
+features across all ten VPN implementations. The matrix covers
+protocol characteristics, cryptographic primitives, NAT traversal
+strategies, routing behavior, and security properties.
+
+The completed feature matrix was published and sent to the respective
+VPN maintainers for review. Maintainer feedback was incorporated as
+corrections and clarifications, improving the accuracy of the final
+classification.
+
 \section{Reproducibility}
 
 Reproducibility is ensured at every layer of the experimental stack.