fix: misc fixes

Feedback from @pooya-rostami

(cherry picked from commit cdbb544)

Author: drupol

src/thesis/1-introduction.typ

@@ -44,10 +44,10 @@ Association for Computing Machinery (ACM) Turing Award Banquet. Since his talk,
 the landscape of software has undergone a radical metamorphosis. The simplicity
 of his advice to #emph[trust people] has become significantly more complex
 in the current era. The modern software supply chain is extensive, often
-encompassing dependencies the often lies beneath the surface. Despite the
-prevalence of open-source software within this supply chain, it is uncommon for
-end-users to compile their own software. As a result, the build systems became a
-prime vector for malicious exploitation
+encompassing dependencies that lies beneath the surface. Despite the prevalence
+of open-source software within this supply chain, it is uncommon for end-users
+to compile their own software. As a result, the build systems became a prime
+vector for malicious exploitation
 #cite(<MarcelFourne2023>, form: "normal", supplement: [p.1]). This underscores
 the vital importance of software reproducibility which ensures that software can
 be reliably built and verified from its source across different environments and
@@ -148,7 +148,7 @@ boy, constantly delving into the mechanics of how things work. This curiosity
 often led to disassembling devices to uncover their hidden secrets, followed by
 a harder quest to reassemble them. While my father played a pivotal role in this
 journey of discovery, and I simply cannot recall a single moment when he
-responded with #emph["I don't know"] it was my mother who truly ignited my
+responded with #emph["I don't know"]; it was my mother who truly ignited my
 path to computers. Her encouragement and unwavering belief in pursuing my
 passions were instrumental in shaping my journey towards a deeper understanding
 of the world around me, especially computers.

src/thesis/2-reproducibility.typ

@@ -1333,7 +1333,7 @@ frequently unattainable in practice.
 
 One of the primary impediments in achieving reproducibility lies in the
 dependency on hardware architecture. Software compiled for different
-architectures, such as `x86` and `ARM,` inherently produces disparate binaries.
+architectures, such as `x86` and `ARM,` inherently produces disparate binaries #cite(<patterson2013>,form:"normal").
 These differences stem from the instruction sets and optimizations that are
 specific to each platform, leading to divergent outputs despite using identical
 source code. This variance highlights a significant reproducibility challenge,

src/thesis/3-tools.typ

@@ -188,7 +188,8 @@ To ensure the robustness and universality of our reproducibility assessment, all
 test scenarios described in this chapter are executed through GitHub Actions
 #cite(<ghActions>, form: "normal"). GitHub Actions is an automation platform
 that enables #gls("CICD"), allowing builds to be performed, tested, and deployed
-across various machines and architectures directly from GitHub repositories.
+across various machines and architectures directly from GitHub repositories
+  #cite(<9978190>,form:"normal").
 
 Our testing environments supports three distinct architectures:
 

src/thesis/literature.bib

@@ -949,3 +949,24 @@ @misc{barba2022definingroleopensource
   primaryClass = {cs.CY},
   url = {https://arxiv.org/abs/2204.12564},
 }
+
+@book{patterson2013,
+  author    = {Patterson, David A. and Hennessy, John L.},
+  title     = {Computer Organization and Design, Fifth Edition: The Hardware/Software Interface},
+  year      = {2013},
+  isbn      = {0124077269},
+  publisher = {Morgan Kaufmann Publishers Inc.},
+  address   = {San Francisco, CA, USA},
+  edition   = {5th},
+  abstract  = {The 5th edition of Computer Organization and Design moves forward into the post-PC era with new examples, exercises, and material highlighting the emergence of mobile computing and the cloud. This generational change is emphasized and explored with updated content featuring tablet computers, cloud infrastructure, and the ARM (mobile computing devices) and x86 (cloud computing) architectures. Because an understanding of modern hardware is essential to achieving good performance and energy efficiency, this edition adds a new concrete example, "Going Faster," used throughout the text to demonstrate extremely effective optimization techniques. Also new to this edition is discussion of the "Eight Great Ideas" of computer architecture. As with previous editions, a MIPS processor is the core used to present the fundamentals of hardware technologies, assembly language, computer arithmetic, pipelining, memory hierarchies and I/O. Instructors looking for4th Edition teaching materials should e-mail textbook@elsevier.com. Includes new examples, exercises, and material highlighting the emergence of mobile computing and the Cloud. Covers parallelism in depth with examples and content highlighting parallel hardware and software topics Features the Intel Core i7, ARM Cortex-A8 and NVIDIA Fermi GPU as real-world examples throughout the book Adds a new concrete example, "Going Faster," to demonstrate how understanding hardware can inspire software optimizations that improve performance by 200 times. Discusses and highlights the "Eight Great Ideas" of computer architecture: Performance via Parallelism; Performance via Pipelining; Performance via Prediction; Design for Moore's Law; Hierarchy of Memories; Abstraction to Simplify Design; Make the Common Case Fast; and Dependability via Redundancy. Includes a full set of updated and improved exercises.}
+}
+
+@inproceedings{9978190,
+  author    = {Decan, Alexandre and Mens, Tom and Mazrae, Pooya Rostami and Golzadeh, Mehdi},
+  booktitle = {2022 IEEE International Conference on Software Maintenance and Evolution (ICSME)},
+  title     = {On the    in Software Development Repositories},
+  year      = {2022},
+  pages     = {235-245},
+  keywords  = {Software maintenance;Automation;Codes;Collaborative software;Ecosystems;Semantics;Collaboration;GitHub Actions;continuous integration;collaborative software development;workflow automation},
+  doi       = {10.1109/ICSME55016.2022.00029}
+}