diff --git a/.obsidian/.obsidian - README.md b/.obsidian/.obsidian - README.md
deleted file mode 100644
index 97128b5f..00000000
--- a/.obsidian/.obsidian - README.md	
+++ /dev/null
@@ -1,24 +0,0 @@
-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/graph.json b/.obsidian/graph.json
index c7d7e9f3..5cb16fe1 100755
--- a/.obsidian/graph.json
+++ b/.obsidian/graph.json
@@ -5,7 +5,7 @@
   "showAttachments": false,
   "hideUnresolved": false,
   "showOrphans": true,
-  "collapse-color-groups": true,
+  "collapse-color-groups": false,
   "colorGroups": [
     {
       "query": "path:\"1 Daily Notes\"  ",
@@ -55,9 +55,16 @@
         "a": 1,
         "rgb": 13922818
       }
+    },
+    {
+      "query": "file:",
+      "color": {
+        "a": 1,
+        "rgb": 11621088
+      }
     }
   ],
-  "collapse-display": true,
+  "collapse-display": false,
   "showArrow": false,
   "textFadeMultiplier": -1.8,
   "nodeSizeMultiplier": 1.79713541666667,
diff --git a/.pandoc/.pandoc - README.md b/.pandoc/.pandoc - README.md
deleted file mode 100644
index 5c8ee1de..00000000
--- a/.pandoc/.pandoc - README.md	
+++ /dev/null
@@ -1,11 +0,0 @@
-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
deleted file mode 100644
index b504e786..00000000
--- a/.trash/.trash - README.md	
+++ /dev/null
@@ -1,43 +0,0 @@
-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/1000s Templates/1000s Templates - README.md b/1000s Templates/1000s Templates - README.md
index 2366556d..bcdfcdcc 100644
--- a/1000s Templates/1000s Templates - README.md	
+++ b/1000s Templates/1000s Templates - README.md	
@@ -3,10 +3,10 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 1000s Templates
 
 ## Files
-- [[Daily Note Template 2.0]]
-- [[Daily Note Template]]
-- [[Heilmeier Catechism]]
-- [[Literature Note]]
-- [[New Note Template]]
-- [[This Past Week Template]]
+- [[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/900s Calendars/0. Deadlines/0. Deadlines - README.md b/900s Calendars/0. Deadlines/0. Deadlines - README.md
index 6ca07302..cc946059 100644
--- a/900s Calendars/0. Deadlines/0. Deadlines - README.md	
+++ b/900s Calendars/0. Deadlines/0. Deadlines - README.md	
@@ -3,12 +3,12 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 0. Deadlines
 
 ## Files
-- [[2024-09-11 Qualifying Exam Abstract Due]]
-- [[2024-09-18 QE Topic Approval]]
-- [[2024-09-19 Working Encrypted Controller]]
-- [[2024-09-23 TRTR Presentation Due]]
-- [[2024-09-30 TRTR Presentation]]
-- [[2024-11-05 Written Proposal First Draft Complete]]
-- [[2024-11-13 QE Proposal Due]]
-- [[2024-12-03 QE Oral Examination]]
+- [[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/900s Calendars/1. Other Work/1. Other Work - README.md b/900s Calendars/1. Other Work/1. Other Work - README.md
index a41de591..f352ff27 100644
--- a/900s Calendars/1. Other Work/1. Other Work - README.md	
+++ b/900s Calendars/1. Other Work/1. Other Work - README.md	
@@ -3,5 +3,5 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 1. Other Work
 
 ## Files
-- [[900s Calendars/1. Other Work/stubb!]]
+- [[stubb!.md]]
 
diff --git a/900s Calendars/2. Research/2. Research - README.md b/900s Calendars/2. Research/2. Research - README.md
index 3457ccf3..b175f465 100644
--- a/900s Calendars/2. Research/2. Research - README.md	
+++ b/900s Calendars/2. Research/2. Research - README.md	
@@ -3,7 +3,7 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 2. Research
 
 ## Files
-- [[2024-08-26 Fighting with the BeagleBone]]
-- [[2024-08-28 HAIS Journal Club]]
-- [[2024-09-10 Nuclear Engineering Steering Committee - Conf Room A UClub]]
+- [[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/900s Calendars/3. Events/3. Events - README.md b/900s Calendars/3. Events/3. Events - README.md
index bc07374e..274c87ed 100644
--- a/900s Calendars/3. Events/3. Events - README.md	
+++ b/900s Calendars/3. Events/3. Events - README.md	
@@ -3,15 +3,15 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 3. Events
 
 ## Files
-- [[2024-08-27 Fighting Parking Ticket]]
-- [[2024-09-14 Pitt vs. WVU]]
-- [[2024-09-18 My Birthday!]]
-- [[2024-09-26 Picnic]]
-- [[2024-09-27 Observatory Visit]]
-- [[2024-10-04 Amber's Parents are Here]]
-- [[2024-10-10 Lane's Bachelor Party]]
-- [[2024-10-23 Michaela's Wedding]]
-- [[2024-11-14 Lane's Wedding]]
-- [[2025-03-02 Spring Break]]
-- [[900s Calendars/3. Events/stubb!]]
+- [[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/900s Calendars/900s Calendars - README.md b/900s Calendars/900s Calendars - README.md
index e6808517..a7f3dc94 100644
--- a/900s Calendars/900s Calendars - README.md	
+++ b/900s Calendars/900s Calendars - README.md	
@@ -3,8 +3,8 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 900s Calendars
 
 ## Subdirectories
-- [[0. Deadlines - README]]
-- [[1. Other Work - README]]
-- [[2. Research - README]]
-- [[3. Events - README]]
+- [[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/9999 Personal/9999 Personal - README.md b/9999 Personal/9999 Personal - README.md
index 194ff88c..1341ab57 100644
--- a/9999 Personal/9999 Personal - README.md	
+++ b/9999 Personal/9999 Personal - README.md	
@@ -3,5 +3,5 @@ Generated by ChatGPT on 2025-02-10
 # Table of Contents for 9999 Personal
 
 ## Files
-- [[Italy Planning]]
+- [[Italy Planning.md]]
 
diff --git a/Dane's Vault - README.md b/Dane's Vault - README.md
deleted file mode 100644
index f50879d3..00000000
--- a/Dane's Vault - README.md	
+++ /dev/null
@@ -1,34 +0,0 @@
-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/NonGraph - README.md b/NonGraph/NonGraph - README.md
index e52ebfaa..e0f4b037 100644
--- a/NonGraph/NonGraph - README.md	
+++ b/NonGraph/NonGraph - README.md	
@@ -2,9 +2,3 @@ Generated by ChatGPT on 2025-02-10
 
 # Table of Contents for NonGraph
 
-## Subdirectories
-- [[1000s Templates - README]]
-- [[2000 Images - README]]
-- [[900s Calendars - README]]
-- [[9999 Personal - README]]
-
diff --git a/reddup.sh b/reddup.sh
index 8898a687..579e4077 100755
--- a/reddup.sh
+++ b/reddup.sh
@@ -4,8 +4,8 @@
 # Generated on: $(date '+%Y-%m-%d')
 #
 # 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 "Folder Name - README.md".
+# and then recursively creates a table-of-contents README file in each
+# non-hidden directory. The file is named "Folder Name - README.md".
 #
 # Each README includes:
 #   - An author/date header.
@@ -15,7 +15,7 @@
 #   - An alphabetically sorted list of immediate files (excluding
 #     the generated README).
 #
-# It is written to handle blank spaces in file and folder names.
+# Hidden directories (e.g., .git) are skipped.
 # ------------------------------------------------------------------
 
 # Delete any existing README files matching "* - README.md"
@@ -24,9 +24,14 @@ find . -type f -name '* - README.md' -delete
 # Set the base directory (change "." if necessary)
 base_dir="."
 
-# Recursively find every directory starting from base_dir.
+# Recursively process every directory starting from base_dir.
 find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
-    # For the top-level directory, use its actual name rather than "."
+    # Skip hidden directories (e.g., those starting with a dot)
+    if [[ "$(basename "$dir")" == .* ]]; then
+        continue
+    fi
+
+    # For the top-level directory (base_dir), use its actual name (using $PWD)
     if [ "$dir" = "$base_dir" ]; then
         base=$(basename "$PWD")
     else
@@ -48,21 +53,21 @@ find "$base_dir" -type d -print0 | while IFS= read -r -d '' dir; do
     # Process Subdirectories
     #########################
     subdirs=()
-    # Find immediate subdirectories (depth 1) in the current directory.
+    # Find immediate subdirectories (depth 1) in the current directory, skipping hidden ones.
     while IFS= read -r -d '' subdir; do
         sub_basename=$(basename "$subdir")
-        # Avoid adding empty names.
         if [ -n "$sub_basename" ]; then
             subdirs+=( "$sub_basename" )
         fi
-    done < <(find "$dir" -mindepth 1 -maxdepth 1 -type d -print0)
+    done < <(find "$dir" -mindepth 1 -maxdepth 1 -type d ! -name '.*' -print0)
 
     if [ ${#subdirs[@]} -gt 0 ]; then
         # Sort subdirectory names alphabetically.
         mapfile -t sorted_subdirs < <(printf "%s\n" "${subdirs[@]}" | sort)
         echo "## Subdirectories" >> "$readme"
         for sub in "${sorted_subdirs[@]}"; do
-            # Build the line as a variable to avoid printf misinterpreting a leading dash.
+            # Build the link to the subdirectory's README file.
+            # The link format is: [[Subfolder/Subfolder - README]]
             line="- [[${sub}/${sub} - README]]"
             printf "%s\n" "$line" >> "$readme"
         done