diff --git a/.obsidian/.obsidian - README.md b/.obsidian/.obsidian - README.md
new file mode 100644
index 000000000..97128b5f4
--- /dev/null
+++ b/.obsidian/.obsidian - README.md	
@@ -0,0 +1,24 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for .obsidian
+
+## Subdirectories
+- [[icons/icons - README]]
+- [[plugins/plugins - README]]
+- [[snippets/snippets - README]]
+- [[themes/themes - README]]
+
+## Files
+- [[appearance.json]]
+- [[app.json]]
+- [[bookmarks.json]]
+- [[community-plugins.json]]
+- [[core-plugins.json]]
+- [[core-plugins-migration.json]]
+- [[daily-notes.json]]
+- [[graph.json]]
+- [[hotkeys.json]]
+- [[templates.json]]
+- [[types.json]]
+- [[workspace.json]]
+
diff --git a/.obsidian/icons/icons - README.md b/.obsidian/icons/icons - README.md
new file mode 100644
index 000000000..ea8c458a5
--- /dev/null
+++ b/.obsidian/icons/icons - README.md	
@@ -0,0 +1,4 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for icons
+
diff --git a/.obsidian/plugins/colored-tags/colored-tags - README.md b/.obsidian/plugins/colored-tags/colored-tags - README.md
new file mode 100644
index 000000000..cc41e6e78
--- /dev/null
+++ b/.obsidian/plugins/colored-tags/colored-tags - README.md	
@@ -0,0 +1,9 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for colored-tags
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+
diff --git a/.obsidian/plugins/dataview/dataview - README.md b/.obsidian/plugins/dataview/dataview - README.md
new file mode 100644
index 000000000..e2f17da70
--- /dev/null
+++ b/.obsidian/plugins/dataview/dataview - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for dataview
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/highlightr-plugin/highlightr-plugin - README.md b/.obsidian/plugins/highlightr-plugin/highlightr-plugin - README.md
new file mode 100644
index 000000000..ddad87c19
--- /dev/null
+++ b/.obsidian/plugins/highlightr-plugin/highlightr-plugin - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for highlightr-plugin
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-admonition/obsidian-admonition - README.md b/.obsidian/plugins/obsidian-admonition/obsidian-admonition - README.md
new file mode 100644
index 000000000..c5797c2f9
--- /dev/null
+++ b/.obsidian/plugins/obsidian-admonition/obsidian-admonition - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-admonition
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-citation-plugin/obsidian-citation-plugin - README.md b/.obsidian/plugins/obsidian-citation-plugin/obsidian-citation-plugin - README.md
new file mode 100644
index 000000000..5822c7623
--- /dev/null
+++ b/.obsidian/plugins/obsidian-citation-plugin/obsidian-citation-plugin - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-citation-plugin
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-enhancing-export/lua/lua - README.md b/.obsidian/plugins/obsidian-enhancing-export/lua/lua - README.md
new file mode 100644
index 000000000..9751a85cc
--- /dev/null
+++ b/.obsidian/plugins/obsidian-enhancing-export/lua/lua - README.md	
@@ -0,0 +1,13 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for lua
+
+## Files
+- [[citefilter.lua]]
+- [[markdown+hugo.lua]]
+- [[markdown.lua]]
+- [[math_block.lua]]
+- [[pdf.lua]]
+- [[polyfill.lua]]
+- [[url.lua]]
+
diff --git a/.obsidian/plugins/obsidian-enhancing-export/obsidian-enhancing-export - README.md b/.obsidian/plugins/obsidian-enhancing-export/obsidian-enhancing-export - README.md
new file mode 100644
index 000000000..f2b51b6fb
--- /dev/null
+++ b/.obsidian/plugins/obsidian-enhancing-export/obsidian-enhancing-export - README.md	
@@ -0,0 +1,14 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-enhancing-export
+
+## Subdirectories
+- [[lua/lua - README]]
+- [[textemplate/textemplate - README]]
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-enhancing-export/textemplate/textemplate - README.md b/.obsidian/plugins/obsidian-enhancing-export/textemplate/textemplate - README.md
new file mode 100644
index 000000000..bf0106437
--- /dev/null
+++ b/.obsidian/plugins/obsidian-enhancing-export/textemplate/textemplate - README.md	
@@ -0,0 +1,9 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for textemplate
+
+## Files
+- [[dissertation.tex]]
+- [[neurips.sty]]
+- [[neurips.tex]]
+
diff --git a/.obsidian/plugins/obsidian-footnotes/obsidian-footnotes - README.md b/.obsidian/plugins/obsidian-footnotes/obsidian-footnotes - README.md
new file mode 100644
index 000000000..163dc2653
--- /dev/null
+++ b/.obsidian/plugins/obsidian-footnotes/obsidian-footnotes - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-footnotes
+
+## Files
+- [[main.js]]
+- [[manifest.json]]
+
diff --git a/.obsidian/plugins/obsidian-full-calendar/obsidian-full-calendar - README.md b/.obsidian/plugins/obsidian-full-calendar/obsidian-full-calendar - README.md
new file mode 100644
index 000000000..7fede8fff
--- /dev/null
+++ b/.obsidian/plugins/obsidian-full-calendar/obsidian-full-calendar - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-full-calendar
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-git/obsidian-git - README.md b/.obsidian/plugins/obsidian-git/obsidian-git - README.md
new file mode 100644
index 000000000..6690373d7
--- /dev/null
+++ b/.obsidian/plugins/obsidian-git/obsidian-git - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-git
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-icon-folder/obsidian-icon-folder - README.md b/.obsidian/plugins/obsidian-icon-folder/obsidian-icon-folder - README.md
new file mode 100644
index 000000000..33382bdc0
--- /dev/null
+++ b/.obsidian/plugins/obsidian-icon-folder/obsidian-icon-folder - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-icon-folder
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-pandoc-reference-list/obsidian-pandoc-reference-list - README.md b/.obsidian/plugins/obsidian-pandoc-reference-list/obsidian-pandoc-reference-list - README.md
new file mode 100644
index 000000000..e2596d680
--- /dev/null
+++ b/.obsidian/plugins/obsidian-pandoc-reference-list/obsidian-pandoc-reference-list - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-pandoc-reference-list
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-style-settings/obsidian-style-settings - README.md b/.obsidian/plugins/obsidian-style-settings/obsidian-style-settings - README.md
new file mode 100644
index 000000000..e5c5cbb79
--- /dev/null
+++ b/.obsidian/plugins/obsidian-style-settings/obsidian-style-settings - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-style-settings
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-tasks-plugin/obsidian-tasks-plugin - README.md b/.obsidian/plugins/obsidian-tasks-plugin/obsidian-tasks-plugin - README.md
new file mode 100644
index 000000000..ba50179aa
--- /dev/null
+++ b/.obsidian/plugins/obsidian-tasks-plugin/obsidian-tasks-plugin - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-tasks-plugin
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/obsidian-zotero-desktop-connector/obsidian-zotero-desktop-connector - README.md b/.obsidian/plugins/obsidian-zotero-desktop-connector/obsidian-zotero-desktop-connector - README.md
new file mode 100644
index 000000000..2f30b9fce
--- /dev/null
+++ b/.obsidian/plugins/obsidian-zotero-desktop-connector/obsidian-zotero-desktop-connector - README.md	
@@ -0,0 +1,11 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for obsidian-zotero-desktop-connector
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[pdfannots2json-linux-x64]]
+- [[styles.css]]
+
diff --git a/.obsidian/plugins/plugins - README.md b/.obsidian/plugins/plugins - README.md
new file mode 100644
index 000000000..7deb15858
--- /dev/null
+++ b/.obsidian/plugins/plugins - README.md	
@@ -0,0 +1,21 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for plugins
+
+## Subdirectories
+- [[colored-tags/colored-tags - README]]
+- [[dataview/dataview - README]]
+- [[highlightr-plugin/highlightr-plugin - README]]
+- [[obsidian-admonition/obsidian-admonition - README]]
+- [[obsidian-citation-plugin/obsidian-citation-plugin - README]]
+- [[obsidian-enhancing-export/obsidian-enhancing-export - README]]
+- [[obsidian-footnotes/obsidian-footnotes - README]]
+- [[obsidian-full-calendar/obsidian-full-calendar - README]]
+- [[obsidian-git/obsidian-git - README]]
+- [[obsidian-icon-folder/obsidian-icon-folder - README]]
+- [[obsidian-pandoc-reference-list/obsidian-pandoc-reference-list - README]]
+- [[obsidian-style-settings/obsidian-style-settings - README]]
+- [[obsidian-tasks-plugin/obsidian-tasks-plugin - README]]
+- [[obsidian-zotero-desktop-connector/obsidian-zotero-desktop-connector - README]]
+- [[templater-obsidian/templater-obsidian - README]]
+
diff --git a/.obsidian/plugins/templater-obsidian/templater-obsidian - README.md b/.obsidian/plugins/templater-obsidian/templater-obsidian - README.md
new file mode 100644
index 000000000..658d26a7a
--- /dev/null
+++ b/.obsidian/plugins/templater-obsidian/templater-obsidian - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for templater-obsidian
+
+## Files
+- [[data.json]]
+- [[main.js]]
+- [[manifest.json]]
+- [[styles.css]]
+
diff --git a/.obsidian/snippets/snippets - README.md b/.obsidian/snippets/snippets - README.md
new file mode 100644
index 000000000..5dab83ebc
--- /dev/null
+++ b/.obsidian/snippets/snippets - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for snippets
+
+## Files
+- [[color_snippet.css]]
+
diff --git a/.obsidian/themes/AnuPpuccin/AnuPpuccin - README.md b/.obsidian/themes/AnuPpuccin/AnuPpuccin - README.md
new file mode 100644
index 000000000..5050c6e21
--- /dev/null
+++ b/.obsidian/themes/AnuPpuccin/AnuPpuccin - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for AnuPpuccin
+
+## Files
+- [[manifest.json]]
+- [[theme.css]]
+
diff --git a/.obsidian/themes/Everforest/Everforest - README.md b/.obsidian/themes/Everforest/Everforest - README.md
new file mode 100644
index 000000000..81fd6dabc
--- /dev/null
+++ b/.obsidian/themes/Everforest/Everforest - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for Everforest
+
+## Files
+- [[manifest.json]]
+- [[theme.css]]
+
diff --git a/.obsidian/themes/Minimal/Minimal - README.md b/.obsidian/themes/Minimal/Minimal - README.md
new file mode 100644
index 000000000..459550d20
--- /dev/null
+++ b/.obsidian/themes/Minimal/Minimal - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for Minimal
+
+## Files
+- [[manifest.json]]
+- [[theme.css]]
+
diff --git a/.obsidian/themes/Obsidian Nord/Obsidian Nord - README.md b/.obsidian/themes/Obsidian Nord/Obsidian Nord - README.md
new file mode 100644
index 000000000..9460223e1
--- /dev/null
+++ b/.obsidian/themes/Obsidian Nord/Obsidian Nord - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for Obsidian Nord
+
+## Files
+- [[manifest.json]]
+- [[theme.css]]
+
diff --git a/.obsidian/themes/themes - README.md b/.obsidian/themes/themes - README.md
new file mode 100644
index 000000000..cf4bd1fb3
--- /dev/null
+++ b/.obsidian/themes/themes - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for themes
+
+## Subdirectories
+- [[AnuPpuccin/AnuPpuccin - README]]
+- [[Everforest/Everforest - README]]
+- [[Minimal/Minimal - README]]
+- [[Obsidian Nord/Obsidian Nord - README]]
+
diff --git a/.pandoc/.pandoc - README.md b/.pandoc/.pandoc - README.md
new file mode 100644
index 000000000..5c8ee1deb
--- /dev/null
+++ b/.pandoc/.pandoc - README.md	
@@ -0,0 +1,11 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for .pandoc
+
+## Files
+- [[apa.csl]]
+- [[ieee.csl]]
+- [[locales-en-US.xml]]
+- [[zotero-library-1.json]]
+- [[zotero-library-2.json]]
+
diff --git a/.trash/.trash - README.md b/.trash/.trash - README.md
new file mode 100644
index 000000000..b504e7862
--- /dev/null
+++ b/.trash/.trash - README.md	
@@ -0,0 +1,43 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for .trash
+
+## Subdirectories
+- [[Untitled/Untitled - README]]
+
+## Files
+- [[2024-08-06.md]]
+- [[2024-08-07.md]]
+- [[2024-08-08.md]]
+- [[2024-08-09 2.md]]
+- [[2024-08-09.md]]
+- [[2024 IEEE Workshop on Security and Resiliency of Critical Infrastructure and Space Technologies (SR-CIST 2.md]]
+- [[2024 IEEE Workshop on Security and Resiliency of Critical Infrastructure and Space Technologies (SR-CIST.md]]
+- [[doing.md]]
+- [[@IntroductionDiffusionModels2022.md]]
+- [[Learn what a vision paper is 2.md]]
+- [[Learn what a vision paper is 3.md]]
+- [[Learn what a vision paper is.md]]
+- [[@maccaroneADVANCEDREACTORCYBER.md]]
+- [[().md]]
+- [[nguyenFuzzyControlSystems2019 2.md]]
+- [[nguyenFuzzyControlSystems2019.md]]
+- [[Notes at.md]]
+- [[@sohl-dicksteinDeepUnsupervisedLearning2015.md]]
+- [[sohl-dicksteinDeepUnsupervisedLearning2015.md]]
+- [[@sunSoKAttacksIndustrial2021.md]]
+- [[Tasks Plugin - Review and check your Statuses 2024-08-06 08-48-38.md]]
+- [[Tasks Plugin - Review and check your Statuses 2024-08-06 08-50-11.md]]
+- [[Tasks Plugin - Review and check your Statuses 2024-08-06 08-51-30.md]]
+- [[Tasks Plugin - Review and check your Statuses 2024-08-06 08-52-11.md]]
+- [[Untitled 1.md]]
+- [[Untitled 2.md]]
+- [[Untitled 3.md]]
+- [[Untitled 4.md]]
+- [[Untitled 5.md]]
+- [[Untitled 6.md]]
+- [[Untitled.canvas]]
+- [[Untitled.md]]
+- [[Weekly Note 2024-08-13.md]]
+- [[Weekly Note 2024-08-21.md]]
+
diff --git a/.trash/Untitled/Untitled - README.md b/.trash/Untitled/Untitled - README.md
new file mode 100644
index 000000000..64781704f
--- /dev/null
+++ b/.trash/Untitled/Untitled - README.md	
@@ -0,0 +1,4 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for Untitled
+
diff --git a/0 Managerial Pages/0 Managerial Pages - README.md b/0 Managerial Pages/0 Managerial Pages - README.md
new file mode 100644
index 000000000..786e8ec3b
--- /dev/null
+++ b/0 Managerial Pages/0 Managerial Pages - README.md	
@@ -0,0 +1,12 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 0 Managerial Pages
+
+## Files
+- [[1 Task Dashboard.md]]
+- [[2025 Spring Enrollment Form.pdf]]
+- [[2. (SR-CIST) Workshop on Security and Resiliency of Critical Infrastructure and Space Technologies.md]]
+- [[2. The_Yellow_Brick_Road_to_a_GRADUATE_degree.ods]]
+- [[To Do List.md]]
+- [[Untitled 1.ods]]
+
diff --git a/1 Daily Notes/1 Daily Notes - README.md b/1 Daily Notes/1 Daily Notes - README.md
new file mode 100644
index 000000000..ca4535b41
--- /dev/null
+++ b/1 Daily Notes/1 Daily Notes - README.md	
@@ -0,0 +1,11 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1 Daily Notes
+
+## Subdirectories
+- [[2024/2024 - README]]
+- [[2025/2025 - README]]
+
+## Files
+- [[Untitled.canvas]]
+
diff --git a/1 Daily Notes/2024/10 October/10 October - README.md b/1 Daily Notes/2024/10 October/10 October - README.md
new file mode 100644
index 000000000..ed8493f87
--- /dev/null
+++ b/1 Daily Notes/2024/10 October/10 October - README.md	
@@ -0,0 +1,29 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 10 October
+
+## Files
+- [[2024-10-01.md]]
+- [[2024-10-02.md]]
+- [[2024-10-03.md]]
+- [[2024-10-04.md]]
+- [[2024-10-07.md]]
+- [[2024-10-08.md]]
+- [[2024-10-09.md]]
+- [[2024-10-10.md]]
+- [[2024-10-11.md]]
+- [[2024-10-14.md]]
+- [[2024-10-15.md]]
+- [[2024-10-16.md]]
+- [[2024-10-17.md]]
+- [[2024-10-18.md]]
+- [[2024-10-21.md]]
+- [[2024-10-22.md]]
+- [[2024-10-23.md]]
+- [[2024-10-24.md]]
+- [[2024-10-25.md]]
+- [[2024-10-28.md]]
+- [[2024-10-29.md]]
+- [[2024-10-30.md]]
+- [[2024-10-31.md]]
+
diff --git a/1 Daily Notes/2024/11 November/11 November - README.md b/1 Daily Notes/2024/11 November/11 November - README.md
new file mode 100644
index 000000000..d3c437109
--- /dev/null
+++ b/1 Daily Notes/2024/11 November/11 November - README.md	
@@ -0,0 +1,20 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 11 November
+
+## Files
+- [[2024-11-01.md]]
+- [[2024-11-04.md]]
+- [[2024-11-05.md]]
+- [[2024-11-06.md]]
+- [[2024-11-07.md]]
+- [[2024-11-08.md]]
+- [[2024-11-11.md]]
+- [[2024-11-12.md]]
+- [[2024-11-13.md]]
+- [[2024-11-14.md]]
+- [[2024-11-15.md]]
+- [[2024-11-18.md]]
+- [[2024-11-19.md]]
+- [[2024-11-20.md]]
+
diff --git a/1 Daily Notes/2024/2024 - README.md b/1 Daily Notes/2024/2024 - README.md
new file mode 100644
index 000000000..4e5e65201
--- /dev/null
+++ b/1 Daily Notes/2024/2024 - README.md	
@@ -0,0 +1,15 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2024
+
+## Subdirectories
+- [[10 October/10 October - README]]
+- [[11 November/11 November - README]]
+- [[8 August/8 August - README]]
+- [[9 September/9 September - README]]
+
+## Files
+- [[2024-12-18.md]]
+- [[2024-12-30.md]]
+- [[2024-12-31.md]]
+
diff --git a/1 Daily Notes/2024/8 August/8 August - README.md b/1 Daily Notes/2024/8 August/8 August - README.md
new file mode 100644
index 000000000..d93857933
--- /dev/null
+++ b/1 Daily Notes/2024/8 August/8 August - README.md	
@@ -0,0 +1,27 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 8 August
+
+## Files
+- [[2024-08-05.md]]
+- [[2024-08-06.md]]
+- [[2024-08-07.md]]
+- [[2024-08-08.md]]
+- [[2024-08-09.md]]
+- [[2024-08-12.md]]
+- [[2024-08-13.md]]
+- [[2024-08-14.md]]
+- [[2024-08-15.md]]
+- [[2024-08-16.md]]
+- [[2024-08-18.md]]
+- [[2024-08-19.md]]
+- [[2024-08-20.md]]
+- [[2024-08-21.md]]
+- [[2024-08-22.md]]
+- [[2024-08-23.md]]
+- [[2024-08-26.md]]
+- [[2024-08-27.md]]
+- [[2024-08-28.md]]
+- [[2024-08-29.md]]
+- [[2024-08-30.md]]
+
diff --git a/1 Daily Notes/2024/9 September/9 September - README.md b/1 Daily Notes/2024/9 September/9 September - README.md
new file mode 100644
index 000000000..d101ad56d
--- /dev/null
+++ b/1 Daily Notes/2024/9 September/9 September - README.md	
@@ -0,0 +1,26 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 9 September
+
+## Files
+- [[2024-09-03.md]]
+- [[2024-09-04.md]]
+- [[2024-09-05.md]]
+- [[2024-09-06.md]]
+- [[2024-09-09.md]]
+- [[2024-09-10.md]]
+- [[2024-09-11.md]]
+- [[2024-09-12.md]]
+- [[2024-09-13.md]]
+- [[2024-09-16.md]]
+- [[2024-09-17.md]]
+- [[2024-09-18.md]]
+- [[2024-09-19.md]]
+- [[2024-09-20.md]]
+- [[2024-09-23.md]]
+- [[2024-09-24.md]]
+- [[2024-09-25.md]]
+- [[2024-09-26.md]]
+- [[2024-09-27.md]]
+- [[2024-09-30.md]]
+
diff --git a/1 Daily Notes/2025/2025 - README.md b/1 Daily Notes/2025/2025 - README.md
new file mode 100644
index 000000000..4830b546e
--- /dev/null
+++ b/1 Daily Notes/2025/2025 - README.md	
@@ -0,0 +1,36 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2025
+
+## Files
+- [[2025-01-01.md]]
+- [[2025-01-02.md]]
+- [[2025-01-03.md]]
+- [[2025-01-06.md]]
+- [[2025-01-07.md]]
+- [[2025-01-08.md]]
+- [[2025-01-09.md]]
+- [[2025-01-10.md]]
+- [[2025-01-13.md]]
+- [[2025-01-14.md]]
+- [[2025-01-15.md]]
+- [[2025-01-16.md]]
+- [[2025-01-17.md]]
+- [[2025-01-20.md]]
+- [[2025-01-21.md]]
+- [[2025-01-22.md]]
+- [[2025-01-23.md]]
+- [[2025-01-24.md]]
+- [[2025-01-26.md]]
+- [[2025-01-27.md]]
+- [[2025-01-28.md]]
+- [[2025-01-29.md]]
+- [[2025-01-30.md]]
+- [[2025-01-31.md]]
+- [[2025-02-03.md]]
+- [[2025-02-04.md]]
+- [[2025-02-05.md]]
+- [[2025-02-06.md]]
+- [[2025-02-07.md]]
+- [[2025-02-10.md]]
+
diff --git a/101 Current Writing/101 Current Writing - README.md b/101 Current Writing/101 Current Writing - README.md
new file mode 100644
index 000000000..696bc2492
--- /dev/null
+++ b/101 Current Writing/101 Current Writing - README.md	
@@ -0,0 +1,11 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 101 Current Writing
+
+## Subdirectories
+- [[ANS NPIC HITL FHE/ANS NPIC HITL FHE - README]]
+
+## Files
+- [[ARCADE Implementation at the University of Pittsburgh.md]]
+- [[Models All The Way Down - A Path Towards Software and Physical System Proof Synergy.md]]
+
diff --git a/101 Current Writing/ANS NPIC HITL FHE/ANS NPIC HITL FHE - README.md b/101 Current Writing/ANS NPIC HITL FHE/ANS NPIC HITL FHE - README.md
new file mode 100644
index 000000000..c1223e73a
--- /dev/null
+++ b/101 Current Writing/ANS NPIC HITL FHE/ANS NPIC HITL FHE - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for ANS NPIC HITL FHE
+
+## Files
+- [[2025-01-24 Where's Everyone At.md]]
+- [[2025-01-29 Rewriting the Experimental Setup Section.md]]
+- [[ANS NPIC Paper Meeting.md]]
+- [[visualization for ANS Paper.md]]
+
diff --git a/199 Paper Notes/199 Paper Notes - README.md b/199 Paper Notes/199 Paper Notes - README.md
new file mode 100644
index 000000000..32d876626
--- /dev/null
+++ b/199 Paper Notes/199 Paper Notes - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 199 Paper Notes
+
+## Files
+- [[Hardware In The Loop Papers.md]]
+
diff --git a/2 Cole Group Meeting Notes/2 Cole Group Meeting Notes - README.md b/2 Cole Group Meeting Notes/2 Cole Group Meeting Notes - README.md
new file mode 100644
index 000000000..3d8ed5046
--- /dev/null
+++ b/2 Cole Group Meeting Notes/2 Cole Group Meeting Notes - README.md	
@@ -0,0 +1,28 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2 Cole Group Meeting Notes
+
+## Files
+- [[Cole Group Monitor Reccomendations.md]]
+- [[Weekly Note 2024-08-07.md]]
+- [[Weekly Note 2024-08-14.md]]
+- [[Weekly Note 2024-08-21.md]]
+- [[Weekly Note 2024-08-29.md]]
+- [[Weekly Note 2024-08-30.md]]
+- [[Weekly Note 2024-09-04.md]]
+- [[Weekly Note 2024-09-11.md]]
+- [[Weekly Note 2024-09-18.md]]
+- [[Weekly Note 2024-09-25.md]]
+- [[Weekly Note 2024-10-02.md]]
+- [[Weekly Note 2024-10-09.md]]
+- [[Weekly Note 2024-10-16.md]]
+- [[Weekly Note 2024-10-23.md]]
+- [[Weekly Note 2024-10-30.md]]
+- [[Weekly Note 2024-11-06.md]]
+- [[Weekly Note 2024-12-11.md]]
+- [[Weekly Note 2025-01-06.md]]
+- [[Weekly Note 2025-01-13.md]]
+- [[Weekly Note 2025-01-20.md]]
+- [[Weekly Note 2025-01-27.md]]
+- [[Weekly Note 2025-02-03.md]]
+
diff --git a/2.1 GSA Meeting Notes/2.1 GSA Meeting Notes - README.md b/2.1 GSA Meeting Notes/2.1 GSA Meeting Notes - README.md
new file mode 100644
index 000000000..4b89d86ad
--- /dev/null
+++ b/2.1 GSA Meeting Notes/2.1 GSA Meeting Notes - README.md	
@@ -0,0 +1,23 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2.1 GSA Meeting Notes
+
+## Subdirectories
+- [[QSG 2025 Sprnig/QSG 2025 Sprnig - README]]
+
+## Files
+- [[2024-09-18.md]]
+- [[2024-09-25.md]]
+- [[2024-09-27 - Questions for Academic Integrity.md]]
+- [[2024-09-30 MoonTree Activity.md]]
+- [[2024-10-04 - QSG.md]]
+- [[2024-10-09.md]]
+- [[2024-10-22 Meeting with Gleeson and Committee Chairs.md]]
+- [[2024-12-13.md]]
+- [[lu19812601pr.tmp]]
+- [[moontree.odp]]
+- [[moontree.odt]]
+- [[moontree.pdf]]
+- [[moontree_supplies.odp]]
+- [[moontree_supplies.pdf]]
+
diff --git a/2.1 GSA Meeting Notes/QSG 2025 Sprnig/QSG 2025 Sprnig - README.md b/2.1 GSA Meeting Notes/QSG 2025 Sprnig/QSG 2025 Sprnig - README.md
new file mode 100644
index 000000000..65d35efd8
--- /dev/null
+++ b/2.1 GSA Meeting Notes/QSG 2025 Sprnig/QSG 2025 Sprnig - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for QSG 2025 Sprnig
+
+## Files
+- [[2025-02-07 - Introduction.md]]
+- [[OLD Qualifier Support Group Plan.md]]
+- [[QSG Poster Notes.md]]
+- [[Qualifier Support Group Plan.md]]
+
diff --git a/200 Library Papers/200 Library Papers - README.md b/200 Library Papers/200 Library Papers - README.md
new file mode 100644
index 000000000..ddb395173
--- /dev/null
+++ b/200 Library Papers/200 Library Papers - README.md	
@@ -0,0 +1,31 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 200 Library Papers
+
+## Files
+- [[aModeladoNucleoAnalisis2023.md]]
+- [[atsumiModifiedBodePlots2012.md]]
+- [[biggsJuryMonolithicOS2018.md]]
+- [[CH4System_Representation_S2020pdf2254.md]]
+- [[doyleFeedbackControlTheory2009.md]]
+- [[doyleGuaranteedMarginsLQG1978.md]]
+- [[farzanRobustControlSynthesis2020.md]]
+- [[fisherHACMSProgramUsing2017a.md]]
+- [[gengSimplifiedReactorModel2024.md]]
+- [[IntroductionDiffusionModels2022.md]]
+- [[kleinFormallyVerifiedSoftware2018.md]]
+- [[Kry10TechnicalOverview.md]]
+- [[matthewsCoupledMultiphysicsSimulations2021.md]]
+- [[matusuRegionsRobustRelative2023.md]]
+- [[ME2046_Sampled_Data_Analysis_Reading_Chapter_2pdf2254ME.md]]
+- [[ME2046_The_z_transform_Chapter_3pdf2254ME.md]]
+- [[mihalicHardwareintheLoopSimulationsHistorical2022.md]]
+- [[My Library.bib]]
+- [[sohl-dicksteinDeepUnsupervisedLearning2015.md]]
+- [[stauffHighFidelityMultiphysicsModeling.md]]
+- [[stevebruntonControlBootcampIntroduction2017.md]]
+- [[stevebruntonControlBootcampLimitations2017.md]]
+- [[stevebruntonControlBootcampSensitivity2017.md]]
+- [[sunSoKAttacksIndustrial2021.md]]
+- [[testoniReviewNuclearMicroreactors2021.md]]
+
diff --git a/201 Metadata/201 Metadata - README.md b/201 Metadata/201 Metadata - README.md
new file mode 100644
index 000000000..5ece08b68
--- /dev/null
+++ b/201 Metadata/201 Metadata - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 201 Metadata
+
+## Files
+- [[ieee.csl]]
+- [[My Library.bib]]
+
diff --git a/3-99 Research/3 ARCADE/1. Ideas for ARCADE Experiments/1. Ideas for ARCADE Experiments - README.md b/3-99 Research/3 ARCADE/1. Ideas for ARCADE Experiments/1. Ideas for ARCADE Experiments - README.md
new file mode 100644
index 000000000..92308aa37
--- /dev/null
+++ b/3-99 Research/3 ARCADE/1. Ideas for ARCADE Experiments/1. Ideas for ARCADE Experiments - README.md	
@@ -0,0 +1,12 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1. Ideas for ARCADE Experiments
+
+## Files
+- [[Digital Twins.md]]
+- [[Fully Homomorphically Encrypted Control.md]]
+- [[KOs Controller.md]]
+- [[Network Delay Effects.md]]
+- [[Plant-Free Controller Development.md]]
+- [[Rust Formally-Proven Embedded Control Code.md]]
+
diff --git a/3-99 Research/3 ARCADE/3 ARCADE - README.md b/3-99 Research/3 ARCADE/3 ARCADE - README.md
new file mode 100644
index 000000000..d76ade76f
--- /dev/null
+++ b/3-99 Research/3 ARCADE/3 ARCADE - README.md	
@@ -0,0 +1,13 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 3 ARCADE
+
+## Subdirectories
+- [[1. Ideas for ARCADE Experiments/1. Ideas for ARCADE Experiments - README]]
+
+## Files
+- [[08-Hahn-ARCADE-Cyber-ModSim-3.pdf]]
+- [[1. A shortlist of ARCADE Experiments.md]]
+- [[Andrew's May 2024 ARCADE Presentation.md]]
+- [[ARCADE Paragraphs for Dan.md]]
+
diff --git a/3-99 Research/3-99 Research - README.md b/3-99 Research/3-99 Research - README.md
new file mode 100644
index 000000000..af9484bab
--- /dev/null
+++ b/3-99 Research/3-99 Research - README.md	
@@ -0,0 +1,16 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 3-99 Research
+
+## Subdirectories
+- [[3 ARCADE/3 ARCADE - README]]
+- [[5 PhD Proposal Ideas/5 PhD Proposal Ideas - README]]
+- [[6 Researching Techniques/6 Researching Techniques - README]]
+- [[7 BeagleBone/7 BeagleBone - README]]
+- [[8.Zotero Web Server/8.Zotero Web Server - README]]
+- [[99 Getting Used to Obsidian/99 Getting Used to Obsidian - README]]
+
+## Files
+- [[Microreactors.md]]
+- [[What is Lobot?.md]]
+
diff --git a/3-99 Research/5 PhD Proposal Ideas/5 PhD Proposal Ideas - README.md b/3-99 Research/5 PhD Proposal Ideas/5 PhD Proposal Ideas - README.md
new file mode 100644
index 000000000..ed1fddd74
--- /dev/null
+++ b/3-99 Research/5 PhD Proposal Ideas/5 PhD Proposal Ideas - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 5 PhD Proposal Ideas
+
+## Files
+- [[1. A Categorized Shortlist of My Ideas.md]]
+- [[A Means to Formally Verify Controller Code Behaves as the Mathematical Model.md]]
+- [[Control Authority Diagram and Management Program.md]]
+- [[Robust Control Inspired Integrity Monitoring System.md]]
+
diff --git a/3-99 Research/6 Researching Techniques/6 Researching Techniques - README.md b/3-99 Research/6 Researching Techniques/6 Researching Techniques - README.md
new file mode 100644
index 000000000..45f6b669b
--- /dev/null
+++ b/3-99 Research/6 Researching Techniques/6 Researching Techniques - README.md	
@@ -0,0 +1,13 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 6 Researching Techniques
+
+## Files
+- [[Highlighting Colors and What they Mean.md]]
+- [[Learning How to Use Github.md]]
+- [[Pandoc and Going from Markdown to LaTeX.md]]
+- [[Setting up a virtual python environment (venv).md]]
+- [[Setting up Neovim for Python.md]]
+- [[Useful VIM commands.md]]
+- [[What is a vision paper (Q).md]]
+
diff --git a/3-99 Research/7 BeagleBone/7 BeagleBone - README.md b/3-99 Research/7 BeagleBone/7 BeagleBone - README.md
new file mode 100644
index 000000000..8e3ceb11b
--- /dev/null
+++ b/3-99 Research/7 BeagleBone/7 BeagleBone - README.md	
@@ -0,0 +1,11 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 7 BeagleBone
+
+## Files
+- [[0 Management.md]]
+- [[1 BeagleBone Setup 😎.md]]
+- [[2 pymodbus On the BeagleBone.md]]
+- [[BeagleBone for ARCADE.md]]
+- [[TRTR Presentation.md]]
+
diff --git a/3-99 Research/8.Zotero Web Server/8.Zotero Web Server - README.md b/3-99 Research/8.Zotero Web Server/8.Zotero Web Server - README.md
new file mode 100644
index 000000000..20661bea4
--- /dev/null
+++ b/3-99 Research/8.Zotero Web Server/8.Zotero Web Server - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 8.Zotero Web Server
+
+## Files
+- [[Set up Zotero Web Server.md]]
+
diff --git a/3-99 Research/99 Getting Used to Obsidian/99 Getting Used to Obsidian - README.md b/3-99 Research/99 Getting Used to Obsidian/99 Getting Used to Obsidian - README.md
new file mode 100644
index 000000000..aa97eb955
--- /dev/null
+++ b/3-99 Research/99 Getting Used to Obsidian/99 Getting Used to Obsidian - README.md	
@@ -0,0 +1,12 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 99 Getting Used to Obsidian
+
+## Files
+- [[Calendar for Obsidian.md]]
+- [[Dataview Tutorial.md]]
+- [[Markdown Cheat Sheet.md]]
+- [[Move Ideas over from Notion.md]]
+- [[Notion to Obsidian Transition.md]]
+- [[Useful Obsidian Docs Links.md]]
+
diff --git a/300s School/300s School - README.md b/300s School/300s School - README.md
new file mode 100644
index 000000000..a2ee85b86
--- /dev/null
+++ b/300s School/300s School - README.md	
@@ -0,0 +1,17 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 300s School
+
+## Subdirectories
+- [[ME 2016 - Nonlinear Dynamical Systems 1/ME 2016 - Nonlinear Dynamical Systems 1 - README]]
+- [[ME 2046 - Digital Control Theory/ME 2046 - Digital Control Theory - README]]
+- [[ME 2085 - Graduate Seminar/ME 2085 - Graduate Seminar - README]]
+- [[ME 2150 - High Assurance Cyber-Physical Systems/ME 2150 - High Assurance Cyber-Physical Systems - README]]
+- [[ME 3100 - Engineering Research and Leadership Management/ME 3100 - Engineering Research and Leadership Management - README]]
+- [[NUCE 2100 - Fundamentals of Nuclear Engineering/NUCE 2100 - Fundamentals of Nuclear Engineering - README]]
+- [[NUCE 2103 - Integration of Plant Systems with the Reactor Core/NUCE 2103 - Integration of Plant Systems with the Reactor Core - README]]
+- [[NUCE 2113 - Radiation Detection and Measurement/NUCE 2113 - Radiation Detection and Measurement - README]]
+
+## Files
+- [[reddup.sh]]
+
diff --git a/300s School/ME 2016 - Nonlinear Dynamical Systems 1/2024-09-09/README - 2024-09-09.md b/300s School/ME 2016 - Nonlinear Dynamical Systems 1/2024-09-09/2024-09-09 - README.md
similarity index 100%
rename from 300s School/ME 2016 - Nonlinear Dynamical Systems 1/2024-09-09/README - 2024-09-09.md
rename to 300s School/ME 2016 - Nonlinear Dynamical Systems 1/2024-09-09/2024-09-09 - README.md
diff --git a/300s School/ME 2016 - Nonlinear Dynamical Systems 1/README - ME 2016 - Nonlinear Dynamical Systems 1.md b/300s School/ME 2016 - Nonlinear Dynamical Systems 1/ME 2016 - Nonlinear Dynamical Systems 1 - README.md
similarity index 88%
rename from 300s School/ME 2016 - Nonlinear Dynamical Systems 1/README - ME 2016 - Nonlinear Dynamical Systems 1.md
rename to 300s School/ME 2016 - Nonlinear Dynamical Systems 1/ME 2016 - Nonlinear Dynamical Systems 1 - README.md
index e07b5c614..1171a05dc 100644
--- a/300s School/ME 2016 - Nonlinear Dynamical Systems 1/README - ME 2016 - Nonlinear Dynamical Systems 1.md	
+++ b/300s School/ME 2016 - Nonlinear Dynamical Systems 1/ME 2016 - Nonlinear Dynamical Systems 1 - README.md	
@@ -3,8 +3,8 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for ME 2016 - Nonlinear Dynamical Systems 1
 
 ## Subdirectories
-- [[2024-09-09/README - 2024-09-09]]
-- [[images/README - images]]
+- [[2024-09-09/2024-09-09 - README]]
+- [[images/images - README]]
 
 ## Files
 - [[2024-08-26 Python Introduction.md]]
@@ -20,6 +20,5 @@ Generated by ChatGPT on 2025-02-10
 - [[2024-12-02 Delay Differential Equation.md]]
 - [[ME2016_MEMS1016___Mini_Project_1.pdf]]
 - [[Mini Project.md]]
-- [[reddup]]
 - [[To Do - ME 2016.md]]
 
diff --git a/300s School/ME 2016 - Nonlinear Dynamical Systems 1/images/README - images.md b/300s School/ME 2016 - Nonlinear Dynamical Systems 1/images/images - README.md
similarity index 100%
rename from 300s School/ME 2016 - Nonlinear Dynamical Systems 1/images/README - images.md
rename to 300s School/ME 2016 - Nonlinear Dynamical Systems 1/images/images - README.md
diff --git a/300s School/ME 2016 - Nonlinear Dynamical Systems 1/reddup b/300s School/ME 2016 - Nonlinear Dynamical Systems 1/reddup
deleted file mode 100644
index e69de29bb..000000000
diff --git a/300s School/ME 2046 - Digital Control Theory/README - ME 2046 - Digital Control Theory.md b/300s School/ME 2046 - Digital Control Theory/ME 2046 - Digital Control Theory - README.md
similarity index 100%
rename from 300s School/ME 2046 - Digital Control Theory/README - ME 2046 - Digital Control Theory.md
rename to 300s School/ME 2046 - Digital Control Theory/ME 2046 - Digital Control Theory - README.md
diff --git a/300s School/ME 2085 - Graduate Seminar/README - ME 2085 - Graduate Seminar.md b/300s School/ME 2085 - Graduate Seminar/ME 2085 - Graduate Seminar - README.md
similarity index 100%
rename from 300s School/ME 2085 - Graduate Seminar/README - ME 2085 - Graduate Seminar.md
rename to 300s School/ME 2085 - Graduate Seminar/ME 2085 - Graduate Seminar - README.md
diff --git a/300s School/ME 2150 - High Assurance Cyber-Physical Systems/README - ME 2150 - High Assurance Cyber-Physical Systems.md b/300s School/ME 2150 - High Assurance Cyber-Physical Systems/ME 2150 - High Assurance Cyber-Physical Systems - README.md
similarity index 100%
rename from 300s School/ME 2150 - High Assurance Cyber-Physical Systems/README - ME 2150 - High Assurance Cyber-Physical Systems.md
rename to 300s School/ME 2150 - High Assurance Cyber-Physical Systems/ME 2150 - High Assurance Cyber-Physical Systems - README.md
diff --git a/300s School/ME 3100 - Engineering Research and Leadership Management/README - ME 3100 - Engineering Research and Leadership Management.md b/300s School/ME 3100 - Engineering Research and Leadership Management/ME 3100 - Engineering Research and Leadership Management - README.md
similarity index 100%
rename from 300s School/ME 3100 - Engineering Research and Leadership Management/README - ME 3100 - Engineering Research and Leadership Management.md
rename to 300s School/ME 3100 - Engineering Research and Leadership Management/ME 3100 - Engineering Research and Leadership Management - README.md
diff --git a/300s School/NUCE 2100 - Fundamentals of Nuclear Engineering/README - NUCE 2100 - Fundamentals of Nuclear Engineering.md b/300s School/NUCE 2100 - Fundamentals of Nuclear Engineering/NUCE 2100 - Fundamentals of Nuclear Engineering - README.md
similarity index 100%
rename from 300s School/NUCE 2100 - Fundamentals of Nuclear Engineering/README - NUCE 2100 - Fundamentals of Nuclear Engineering.md
rename to 300s School/NUCE 2100 - Fundamentals of Nuclear Engineering/NUCE 2100 - Fundamentals of Nuclear Engineering - README.md
diff --git a/300s School/NUCE 2103 - Integration of Plant Systems with the Reactor Core/README - NUCE 2103 - Integration of Plant Systems with the Reactor Core.md b/300s School/NUCE 2103 - Integration of Plant Systems with the Reactor Core/NUCE 2103 - Integration of Plant Systems with the Reactor Core - README.md
similarity index 100%
rename from 300s School/NUCE 2103 - Integration of Plant Systems with the Reactor Core/README - NUCE 2103 - Integration of Plant Systems with the Reactor Core.md
rename to 300s School/NUCE 2103 - Integration of Plant Systems with the Reactor Core/NUCE 2103 - Integration of Plant Systems with the Reactor Core - README.md
diff --git a/300s School/NUCE 2113 - Radiation Detection and Measurement/README - NUCE 2113 - Radiation Detection and Measurement.md b/300s School/NUCE 2113 - Radiation Detection and Measurement/NUCE 2113 - Radiation Detection and Measurement - README.md
similarity index 100%
rename from 300s School/NUCE 2113 - Radiation Detection and Measurement/README - NUCE 2113 - Radiation Detection and Measurement.md
rename to 300s School/NUCE 2113 - Radiation Detection and Measurement/NUCE 2113 - Radiation Detection and Measurement - README.md
diff --git a/300s School/README - ..md b/300s School/README - ..md
deleted file mode 100644
index 9201a4696..000000000
--- a/300s School/README - ..md	
+++ /dev/null
@@ -1,18 +0,0 @@
-Generated by ChatGPT on 2025-02-10
-
-# Table of Contents for .
-
-## Subdirectories
-- [[ME 2016 - Nonlinear Dynamical Systems 1/README - ME 2016 - Nonlinear Dynamical Systems 1]]
-- [[ME 2046 - Digital Control Theory/README - ME 2046 - Digital Control Theory]]
-- [[ME 2085 - Graduate Seminar/README - ME 2085 - Graduate Seminar]]
-- [[ME 2150 - High Assurance Cyber-Physical Systems/README - ME 2150 - High Assurance Cyber-Physical Systems]]
-- [[ME 3100 - Engineering Research and Leadership Management/README - ME 3100 - Engineering Research and Leadership Management]]
-- [[NUCE 2100 - Fundamentals of Nuclear Engineering/README - NUCE 2100 - Fundamentals of Nuclear Engineering]]
-- [[NUCE 2103 - Integration of Plant Systems with the Reactor Core/README - NUCE 2103 - Integration of Plant Systems with the Reactor Core]]
-- [[NUCE 2113 - Radiation Detection and Measurement/README - NUCE 2113 - Radiation Detection and Measurement]]
-
-## Files
-- [[']]
-- [[reddup.sh]]
-
diff --git a/300s School/reddup.sh b/300s School/reddup.sh
index 5042b6687..5076a3d43 100755
--- a/300s School/reddup.sh	
+++ b/300s School/reddup.sh	
@@ -3,9 +3,9 @@
 # Author: ChatGPT
 # Generated on: $(date '+%Y-%m-%d')
 #
-# This script deletes existing README files matching "README - *.md"
+# This script deletes existing README files matching "* - README.md"
 # and then recursively creates a table-of-contents README file in
-# each directory. The file is named "README - {Folder Name}.md".
+# each directory. The file is named "Folder Name - README.md".
 #
 # Each README includes:
 #   - An author/date header.
@@ -18,22 +18,26 @@
 # It is written to handle blank spaces in file and folder names.
 # ------------------------------------------------------------------
 
-# Delete any existing README files matching "README - *.md"
-find . -type f -name 'README - *.md' -delete
+# Delete any existing README files matching "* - README.md"
+find . -type f -name '* - README.md' -delete
 
 # Set the base directory (change "." if necessary)
 base_dir="."
 
 # Recursively find every directory starting from base_dir.
 find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
-    # Get the folder's base name (handles spaces correctly)
-    base=$(basename "$dir")
-    # Define the path for the README file: "README - {Folder Name}.md"
-    readme="$dir/README - ${base}.md"
+    # For the top-level directory, use its actual name rather than "."
+    if [ "$dir" = "$base_dir" ]; then
+        base=$(basename "$PWD")
+    else
+        base=$(basename "$dir")
+    fi
+
+    # Define the path for the README file: "Folder Name - README.md"
+    readme="!$dir/${base} - README.md"
 
     # Write the header into the README file, including author/date attribution.
     {
-      echo "Generated by ChatGPT on $(date '+%Y-%m-%d')"
       echo ""
       echo "# Table of Contents for ${base}"
       echo ""
@@ -45,17 +49,21 @@ find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
     subdirs=()
     # Find immediate subdirectories (depth 1) in the current directory.
     while IFS= read -r -d '' subdir; do
-        subdirs+=( "$(basename "$subdir")" )
+        sub_basename=$(basename "$subdir")
+        # Avoid adding empty names.
+        if [ -n "$sub_basename" ]; then
+            subdirs+=( "$sub_basename" )
+        fi
     done < <(find "$dir" -mindepth 1 -maxdepth 1 -type d -print0)
 
     if [ ${#subdirs[@]} -gt 0 ]; then
-        # Sort subdirectory names alphabetically while preserving spaces.
+        # Sort subdirectory names alphabetically.
         mapfile -t sorted_subdirs < <(printf "%s\n" "${subdirs[@]}" | sort)
         echo "## Subdirectories" >> "$readme"
         for sub in "${sorted_subdirs[@]}"; do
-            # Link to the subdirectory's README file.
-            # The link format: [[Subfolder/README - Subfolder]]
-            echo "- [[${sub}/README - ${sub}]]" >> "$readme"
+            # Build the line as a variable to avoid printf misinterpreting a leading dash.
+            line="- [[${sub}/${sub} - README]]"
+            printf "%s\n" "$line" >> "$readme"
         done
         echo "" >> "$readme"
     fi
@@ -66,15 +74,19 @@ find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
     files=()
     # Find immediate files (depth 1), excluding the generated README file.
     while IFS= read -r -d '' file; do
-        files+=( "$(basename "$file")" )
+        fbase=$(basename "$file")
+        if [ -n "$fbase" ]; then
+            files+=( "$fbase" )
+        fi
     done < <(find "$dir" -mindepth 1 -maxdepth 1 -type f ! -path "$readme" -print0)
 
     if [ ${#files[@]} -gt 0 ]; then
-        # Sort file names alphabetically while preserving spaces.
+        # Sort file names alphabetically.
         mapfile -t sorted_files < <(printf "%s\n" "${files[@]}" | sort)
         echo "## Files" >> "$readme"
         for f in "${sorted_files[@]}"; do
-            echo "- [[${f}]]" >> "$readme"
+            line="- [[${f}]]"
+            printf "%s\n" "$line" >> "$readme"
         done
         echo "" >> "$readme"
     fi
diff --git a/4 Qualifying Exam/0 Overview/0 Overview - README.md b/4 Qualifying Exam/0 Overview/0 Overview - README.md
new file mode 100644
index 000000000..adb7e1b7d
--- /dev/null
+++ b/4 Qualifying Exam/0 Overview/0 Overview - README.md	
@@ -0,0 +1,9 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 0 Overview
+
+## Files
+- [[0. QE Overview.md]]
+- [[ME_PhD_Qualifying_Exam_Guideline_Fall2024.pdf]]
+- [[Notes from first Info Session.md]]
+
diff --git a/4 Qualifying Exam/1 Managing Stuff/1 Managing Stuff - README.md b/4 Qualifying Exam/1 Managing Stuff/1 Managing Stuff - README.md
new file mode 100644
index 000000000..dd3df9636
--- /dev/null
+++ b/4 Qualifying Exam/1 Managing Stuff/1 Managing Stuff - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1 Managing Stuff
+
+## Files
+- [[0. QE To Do List.md]]
+- [[How things will be organized.md]]
+- [[Outstanding Tasks.md]]
+- [[QE Research Questions.md]]
+
diff --git a/4 Qualifying Exam/2 Writing/2 Writing - README.md b/4 Qualifying Exam/2 Writing/2 Writing - README.md
new file mode 100644
index 000000000..9d523718e
--- /dev/null
+++ b/4 Qualifying Exam/2 Writing/2 Writing - README.md	
@@ -0,0 +1,20 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2 Writing
+
+## Files
+- [[0. QE Abstract.md]]
+- [[1. QE Goals and Outcomes.md]]
+- [[2. QE State of the Art.md]]
+- [[3. QE Research Approach.md]]
+- [[4. QE Broader Impacts.md]]
+- [[5. QE Metrics of Success.md]]
+- [[6. QE Risks and Contingencies.md]]
+- [[7. QE One Pager.md]]
+- [[8. QE Oral Exam Presentation.md]]
+- [[QE Abstract For Dan.md]]
+- [[QE Abstract For Dan.tex]]
+- [[test.bib]]
+- [[Untitled.bib]]
+- [[Untitled.tex]]
+
diff --git a/4 Qualifying Exam/3 Notes/3 Notes - README.md b/4 Qualifying Exam/3 Notes/3 Notes - README.md
new file mode 100644
index 000000000..334d07948
--- /dev/null
+++ b/4 Qualifying Exam/3 Notes/3 Notes - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 3 Notes
+
+## Files
+- [[Feedback Control Theory.md]]
+- [[How is robust control validation done?.md]]
+- [[Robust Control.md]]
+- [[What is gain scheduling?.md]]
+
diff --git a/4 Qualifying Exam/4 Presentation/4 Presentation - README.md b/4 Qualifying Exam/4 Presentation/4 Presentation - README.md
new file mode 100644
index 000000000..91f754bbf
--- /dev/null
+++ b/4 Qualifying Exam/4 Presentation/4 Presentation - README.md	
@@ -0,0 +1,9 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 4 Presentation
+
+## Files
+- [[Building the Slides.md]]
+- [[Outline.md]]
+- [[Presentation Tasks.md]]
+
diff --git a/4 Qualifying Exam/4 Qualifying Exam - README.md b/4 Qualifying Exam/4 Qualifying Exam - README.md
new file mode 100644
index 000000000..3bd17e258
--- /dev/null
+++ b/4 Qualifying Exam/4 Qualifying Exam - README.md	
@@ -0,0 +1,18 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 4 Qualifying Exam
+
+## Subdirectories
+- [[0 Overview/0 Overview - README]]
+- [[1 Managing Stuff/1 Managing Stuff - README]]
+- [[2 Writing/2 Writing - README]]
+- [[3 Notes/3 Notes - README]]
+- [[4 Presentation/4 Presentation - README]]
+- [[98 With Revisions/98 With Revisions - README]]
+- [[99 Exports/99 Exports - README]]
+
+## Files
+- [[QE_Application_Sabo.pdf]]
+- [[qualifying_exam_application_form.docx]]
+- [[qualifying_exam_application_form_filled.docx]]
+
diff --git a/4 Qualifying Exam/98 With Revisions/98 With Revisions - README.md b/4 Qualifying Exam/98 With Revisions/98 With Revisions - README.md
new file mode 100644
index 000000000..4044b1b7f
--- /dev/null
+++ b/4 Qualifying Exam/98 With Revisions/98 With Revisions - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 98 With Revisions
+
+## Files
+- [[QE Abstract For Dan_COMMENTS.pdf]]
+
diff --git a/4 Qualifying Exam/99 Exports/99 Exports - README.md b/4 Qualifying Exam/99 Exports/99 Exports - README.md
new file mode 100644
index 000000000..4622a73cd
--- /dev/null
+++ b/4 Qualifying Exam/99 Exports/99 Exports - README.md	
@@ -0,0 +1,8 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 99 Exports
+
+## Files
+- [[QE Abstract For Dan_v1.pdf]]
+- [[QE Abstract For Dan_v2.pdf]]
+
diff --git a/5 Thesis/1 Ideas/1 Ideas - README.md b/5 Thesis/1 Ideas/1 Ideas - README.md
new file mode 100644
index 000000000..3b53abfc2
--- /dev/null
+++ b/5 Thesis/1 Ideas/1 Ideas - README.md	
@@ -0,0 +1,4 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1 Ideas
+
diff --git a/5 Thesis/2 Logs/2 Logs - README.md b/5 Thesis/2 Logs/2 Logs - README.md
new file mode 100644
index 000000000..9f22835d1
--- /dev/null
+++ b/5 Thesis/2 Logs/2 Logs - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2 Logs
+
+## Files
+- [[2025-01 Thesis Log.md]]
+
diff --git a/5 Thesis/3 Notes/3 Notes - README.md b/5 Thesis/3 Notes/3 Notes - README.md
new file mode 100644
index 000000000..98d6e0449
--- /dev/null
+++ b/5 Thesis/3 Notes/3 Notes - README.md	
@@ -0,0 +1,4 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 3 Notes
+
diff --git a/5 Thesis/5 Thesis - README.md b/5 Thesis/5 Thesis - README.md
new file mode 100644
index 000000000..6df93b704
--- /dev/null
+++ b/5 Thesis/5 Thesis - README.md	
@@ -0,0 +1,13 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 5 Thesis
+
+## Subdirectories
+- [[1 Ideas/1 Ideas - README]]
+- [[2 Logs/2 Logs - README]]
+- [[3 Notes/3 Notes - README]]
+
+## Files
+- [[Thesis Thoughts.md]]
+- [[Things to Do.md]]
+
diff --git a/Dane's Vault - README.md b/Dane's Vault - README.md
new file mode 100644
index 000000000..f50879d37
--- /dev/null
+++ b/Dane's Vault - README.md	
@@ -0,0 +1,34 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for Dane's Vault
+
+## Subdirectories
+- [[0 Managerial Pages/0 Managerial Pages - README]]
+- [[101 Current Writing/101 Current Writing - README]]
+- [[199 Paper Notes/199 Paper Notes - README]]
+- [[1 Daily Notes/1 Daily Notes - README]]
+- [[200 Library Papers/200 Library Papers - README]]
+- [[201 Metadata/201 Metadata - README]]
+- [[2.1 GSA Meeting Notes/2.1 GSA Meeting Notes - README]]
+- [[2 Cole Group Meeting Notes/2 Cole Group Meeting Notes - README]]
+- [[300s School/300s School - README]]
+- [[3-99 Research/3-99 Research - README]]
+- [[4 Qualifying Exam/4 Qualifying Exam - README]]
+- [[5 Thesis/5 Thesis - README]]
+- [[.git/.git - README]]
+- [[NonGraph/NonGraph - README]]
+- [[.obsidian/.obsidian - README]]
+- [[.pandoc/.pandoc - README]]
+- [[.trash/.trash - README]]
+
+## Files
+- [[1002_Goals_and_Outcomes.docx]]
+- [[Final Exam 2103 Summer 2024.docx]]
+- [[giter_done.sh]]
+- [[.gitignore]]
+- [[NUCE.md]]
+- [[Random things I found that I should look into.md]]
+- [[reddup.sh]]
+- [[test.md]]
+- [[Union Pitch to Persians.md]]
+
diff --git a/NonGraph/1000s Templates/1000s Templates - README.md b/NonGraph/1000s Templates/1000s Templates - README.md
new file mode 100644
index 000000000..bcdfcdcca
--- /dev/null
+++ b/NonGraph/1000s Templates/1000s Templates - README.md	
@@ -0,0 +1,12 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1000s Templates
+
+## Files
+- [[Daily Note Template 2.0.md]]
+- [[Daily Note Template.md]]
+- [[Heilmeier Catechism.md]]
+- [[Literature Note.md]]
+- [[New Note Template.md]]
+- [[This Past Week Template.md]]
+
diff --git a/NonGraph/2000 Images/2000 Images - README.md b/NonGraph/2000 Images/2000 Images - README.md
new file mode 100644
index 000000000..4e4b1c40c
--- /dev/null
+++ b/NonGraph/2000 Images/2000 Images - README.md	
@@ -0,0 +1,18 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2000 Images
+
+## Files
+- [[Pasted image 20241012132644.png]]
+- [[Pasted image 20241012135404.png]]
+- [[Pasted image 20241014145054.png]]
+- [[Pasted image 20241015172652.png]]
+- [[Pasted image 20241015172708.png]]
+- [[Pasted image 20241021155046.png]]
+- [[Pasted image 20241028151006.png]]
+- [[Pasted image 20241028151117.png]]
+- [[Pasted image 20241028152704.png]]
+- [[Pasted image 20250109181319.png]]
+- [[Pasted image 20250116160940.png]]
+- [[Pasted image 20250116161008.png]]
+
diff --git a/NonGraph/900s Calendars/0. Deadlines/0. Deadlines - README.md b/NonGraph/900s Calendars/0. Deadlines/0. Deadlines - README.md
new file mode 100644
index 000000000..cc946059c
--- /dev/null
+++ b/NonGraph/900s Calendars/0. Deadlines/0. Deadlines - README.md	
@@ -0,0 +1,14 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 0. Deadlines
+
+## Files
+- [[2024-09-11 Qualifying Exam Abstract Due.md]]
+- [[2024-09-18 QE Topic Approval.md]]
+- [[2024-09-19 Working Encrypted Controller.md]]
+- [[2024-09-23 TRTR Presentation Due.md]]
+- [[2024-09-30 TRTR Presentation.md]]
+- [[2024-11-05 Written Proposal First Draft Complete.md]]
+- [[2024-11-13 QE Proposal Due.md]]
+- [[2024-12-03 QE Oral Examination.md]]
+
diff --git a/NonGraph/900s Calendars/1. Other Work/1. Other Work - README.md b/NonGraph/900s Calendars/1. Other Work/1. Other Work - README.md
new file mode 100644
index 000000000..f352ff274
--- /dev/null
+++ b/NonGraph/900s Calendars/1. Other Work/1. Other Work - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 1. Other Work
+
+## Files
+- [[stubb!.md]]
+
diff --git a/NonGraph/900s Calendars/2. Research/2. Research - README.md b/NonGraph/900s Calendars/2. Research/2. Research - README.md
new file mode 100644
index 000000000..b175f4651
--- /dev/null
+++ b/NonGraph/900s Calendars/2. Research/2. Research - README.md	
@@ -0,0 +1,9 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 2. Research
+
+## Files
+- [[2024-08-26 Fighting with the BeagleBone.md]]
+- [[2024-08-28 HAIS Journal Club.md]]
+- [[2024-09-10 Nuclear Engineering Steering Committee - Conf Room A UClub.md]]
+
diff --git a/NonGraph/900s Calendars/3. Events/3. Events - README.md b/NonGraph/900s Calendars/3. Events/3. Events - README.md
new file mode 100644
index 000000000..274c87ede
--- /dev/null
+++ b/NonGraph/900s Calendars/3. Events/3. Events - README.md	
@@ -0,0 +1,17 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 3. Events
+
+## Files
+- [[2024-08-27 Fighting Parking Ticket.md]]
+- [[2024-09-14 Pitt vs. WVU.md]]
+- [[2024-09-18 My Birthday!.md]]
+- [[2024-09-26 Picnic.md]]
+- [[2024-09-27 Observatory Visit.md]]
+- [[2024-10-04 Amber's Parents are Here.md]]
+- [[2024-10-10 Lane's Bachelor Party.md]]
+- [[2024-10-23 Michaela's Wedding.md]]
+- [[2024-11-14 Lane's Wedding.md]]
+- [[2025-03-02 Spring Break.md]]
+- [[stubb!.md]]
+
diff --git a/NonGraph/900s Calendars/900s Calendars - README.md b/NonGraph/900s Calendars/900s Calendars - README.md
new file mode 100644
index 000000000..a7f3dc941
--- /dev/null
+++ b/NonGraph/900s Calendars/900s Calendars - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 900s Calendars
+
+## Subdirectories
+- [[0. Deadlines/0. Deadlines - README]]
+- [[1. Other Work/1. Other Work - README]]
+- [[2. Research/2. Research - README]]
+- [[3. Events/3. Events - README]]
+
diff --git a/NonGraph/9999 Personal/9999 Personal - README.md b/NonGraph/9999 Personal/9999 Personal - README.md
new file mode 100644
index 000000000..1341ab577
--- /dev/null
+++ b/NonGraph/9999 Personal/9999 Personal - README.md	
@@ -0,0 +1,7 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for 9999 Personal
+
+## Files
+- [[Italy Planning.md]]
+
diff --git a/NonGraph/NonGraph - README.md b/NonGraph/NonGraph - README.md
new file mode 100644
index 000000000..1508866d4
--- /dev/null
+++ b/NonGraph/NonGraph - README.md	
@@ -0,0 +1,10 @@
+Generated by ChatGPT on 2025-02-10
+
+# Table of Contents for NonGraph
+
+## Subdirectories
+- [[1000s Templates/1000s Templates - README]]
+- [[2000 Images/2000 Images - README]]
+- [[900s Calendars/900s Calendars - README]]
+- [[9999 Personal/9999 Personal - README]]
+
diff --git a/300s School/' b/reddup.sh
old mode 100644
new mode 100755
similarity index 64%
rename from 300s School/'
rename to reddup.sh
index aed4a093d..8898a6876
--- a/300s School/'	
+++ b/reddup.sh
@@ -1,12 +1,11 @@
-
 #!/bin/bash
 # ------------------------------------------------------------------
 # Author: ChatGPT
 # Generated on: $(date '+%Y-%m-%d')
 #
-# This script deletes existing README files matching "README - *.md"
+# This script deletes existing README files matching "* - README.md"
 # and then recursively creates a table-of-contents README file in
-# each directory. The file is named "README - {Folder Name}.md".
+# each directory. The file is named "Folder Name - README.md".
 #
 # Each README includes:
 #   - An author/date header.
@@ -19,18 +18,23 @@
 # It is written to handle blank spaces in file and folder names.
 # ------------------------------------------------------------------
 
-# Delete any existing README files matching "README - *.md"
-find . -type f -name 'README - *.md' -delete
+# Delete any existing README files matching "* - README.md"
+find . -type f -name '* - README.md' -delete
 
 # Set the base directory (change "." if necessary)
 base_dir="."
 
 # Recursively find every directory starting from base_dir.
 find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
-    # Get the folder's base name (handles spaces correctly)
-    base=$(basename "$dir")
-    # Define the path for the README file: "README - {Folder Name}.md"
-    readme="$dir/README - ${base}.md"
+    # For the top-level directory, use its actual name rather than "."
+    if [ "$dir" = "$base_dir" ]; then
+        base=$(basename "$PWD")
+    else
+        base=$(basename "$dir")
+    fi
+
+    # Define the path for the README file: "Folder Name - README.md"
+    readme="$dir/${base} - README.md"
 
     # Write the header into the README file, including author/date attribution.
     {
@@ -46,17 +50,21 @@ find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
     subdirs=()
     # Find immediate subdirectories (depth 1) in the current directory.
     while IFS= read -r -d '' subdir; do
-        subdirs+=( "$(basename "$subdir")" )
+        sub_basename=$(basename "$subdir")
+        # Avoid adding empty names.
+        if [ -n "$sub_basename" ]; then
+            subdirs+=( "$sub_basename" )
+        fi
     done < <(find "$dir" -mindepth 1 -maxdepth 1 -type d -print0)
 
     if [ ${#subdirs[@]} -gt 0 ]; then
-        # Sort subdirectory names alphabetically while preserving spaces.
+        # Sort subdirectory names alphabetically.
         mapfile -t sorted_subdirs < <(printf "%s\n" "${subdirs[@]}" | sort)
         echo "## Subdirectories" >> "$readme"
         for sub in "${sorted_subdirs[@]}"; do
-            # Link to the subdirectory's README file.
-            # The link format: [[Subfolder/README - Subfolder]]
-            echo "- [[${sub}/README - ${sub}]]" >> "$readme"
+            # Build the line as a variable to avoid printf misinterpreting a leading dash.
+            line="- [[${sub}/${sub} - README]]"
+            printf "%s\n" "$line" >> "$readme"
         done
         echo "" >> "$readme"
     fi
@@ -67,15 +75,19 @@ find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
     files=()
     # Find immediate files (depth 1), excluding the generated README file.
     while IFS= read -r -d '' file; do
-        files+=( "$(basename "$file")" )
+        fbase=$(basename "$file")
+        if [ -n "$fbase" ]; then
+            files+=( "$fbase" )
+        fi
     done < <(find "$dir" -mindepth 1 -maxdepth 1 -type f ! -path "$readme" -print0)
 
     if [ ${#files[@]} -gt 0 ]; then
-        # Sort file names alphabetically while preserving spaces.
+        # Sort file names alphabetically.
         mapfile -t sorted_files < <(printf "%s\n" "${files[@]}" | sort)
         echo "## Files" >> "$readme"
         for f in "${sorted_files[@]}"; do
-            echo "- [[${f}]]" >> "$readme"
+            line="- [[${f}]]"
+            printf "%s\n" "$line" >> "$readme"
         done
         echo "" >> "$readme"
     fi