add a new supplementary on bugs and issues

Author: DininduSenanayake

docs/5.from_git_to_github.md

@@ -242,56 +242,6 @@ flowchart TB
     - **Request specific reviewers** — tag people with expertise
     - **Respond to feedback** — science is iterative!
 
----
-
-## 7. Issues — Tracking Bugs and Ideas
-
-A user tries the pipeline and finds a bug. Instead of emailing, they open an **Issue**:
-
-### On GitHub:
-1. Click **"Issues"** → **"New issue"**
-2. Title: `Error in QC filtering with empty cells`
-3. Description:
-````markdown
-   ## Bug description
-   When running `qc_filtering.py` on a dataset with empty droplets, 
-   the script crashes with:
-````
-   IndexError: list index out of range
-````
-   
-   ## Steps to reproduce
-   1. Load dataset with empty cells: `adata = load_data("empty_drops.h5ad")`
-   2. Run: `qc_filtering.py --min-genes 200`
-   
-   ## Expected behavior
-   Should filter out empty cells without crashing
-   
-   ## System info
-   - Python 3.9
-   - scanpy 1.9.1
-````
-4. Add labels: `bug`, `priority:high`
-5. Submit issue (#15)
-
-Dr. X sees the issue, creates a branch `fix-empty-cells`, fixes the bug, and references it in the commit:
-````bash
-git commit -m "Fix QC filtering for empty cells (fixes #15)"
-````
-
-When merged, issue #15 automatically closes!
-````mermaid
-flowchart LR
-  A[User finds bug] --> B[Open Issue #15]
-  B --> C[Dr. X creates fix-empty-cells branch]
-  C --> D[Commit: 'fixes #15']
-  D --> E[Pull Request]
-  E --> F[Merge to main]
-  F --> G[Issue #15 auto-closes]
-  
-  style B fill:#ffe6e6,stroke:#f00
-  style G fill:#e6ffe6,stroke:#0a0
-````
 
 ---
 

docs/supplementary/3.issues_and_bug_tracking.md

@@ -0,0 +1,48 @@
+# Issues — Tracking Bugs and Ideas
+
+A user tries the pipeline and finds a bug. Instead of emailing, they open an **Issue**:
+
+### On GitHub:
+1. Click **"Issues"** → **"New issue"**
+2. Title: `Error in QC filtering with empty cells`
+3. Description:
+````markdown
+   ## Bug description
+   When running `qc_filtering.py` on a dataset with empty droplets, 
+   the script crashes with:
+````
+   IndexError: list index out of range
+````
+   
+   ## Steps to reproduce
+   1. Load dataset with empty cells: `adata = load_data("empty_drops.h5ad")`
+   2. Run: `qc_filtering.py --min-genes 200`
+   
+   ## Expected behavior
+   Should filter out empty cells without crashing
+   
+   ## System info
+   - Python 3.9
+   - scanpy 1.9.1
+````
+4. Add labels: `bug`, `priority:high`
+5. Submit issue (#15)
+
+Dr. X sees the issue, creates a branch `fix-empty-cells`, fixes the bug, and references it in the commit:
+````bash
+git commit -m "Fix QC filtering for empty cells (fixes #15)"
+````
+
+When merged, issue #15 automatically closes!
+````mermaid
+flowchart LR
+  A[User finds bug] --> B[Open Issue #15]
+  B --> C[Dr. X creates fix-empty-cells branch]
+  C --> D[Commit: 'fixes #15']
+  D --> E[Pull Request]
+  E --> F[Merge to main]
+  F --> G[Issue #15 auto-closes]
+  
+  style B fill:#ffe6e6,stroke:#f00
+  style G fill:#e6ffe6,stroke:#0a0
+````