fix: upgrade Gradio SDK to 6.0.1 and add fill_height for HF Spaces UI fix

Root cause: HuggingFace Spaces was deploying with sdk_version 5.33.0,
but the UI cutoff bug (top content hidden beneath HF banner) was fixed
in Gradio 5.36 via PR #11427.

Changes:
- README.md: sdk_version "5.33.0" → "6.0.1" (latest stable)
- src/app.py: Added fill_height=True to gr.Blocks() for proper layout
- docs/bugs/001_gradio_ui_cutoff.md: Full investigation documentation

Fixes #31

References:
- https://github.com/gradio-app/gradio/issues/11417
- https://github.com/gradio-app/gradio/pull/11427

README.md

@@ -4,7 +4,7 @@ emoji: 🧬
 colorFrom: blue
 colorTo: purple
 sdk: gradio
-sdk_version: "5.33.0"
+sdk_version: "6.0.1"
 python_version: "3.11"
 app_file: src/app.py
 pinned: false

docs/bugs/001_gradio_ui_cutoff.md

@@ -0,0 +1,135 @@
+# BUG-001: Gradio UI Header Cut Off on HuggingFace Spaces
+
+**Status:** 🟡 Fix Implemented (Pending Deploy)
+**Severity:** Medium (UI/UX)
+**Reported:** 2025-11-26
+**Branch:** `fix/gradio-ui-scrolling`
+**Related GitHub Issue:** #31
+
+---
+
+## Problem Description
+
+The top portion of the Gradio app (title, description, markdown blocks) is cut off and hidden beneath the HuggingFace Spaces banner. Users cannot scroll up to see this content.
+
+**Symptoms:**
+- Top content (title "🧬 DeepCritical", description) invisible
+- Unable to scroll up to see hidden content
+- Issue disappears when resizing browser or zooming in/out
+- Most prominent on mobile devices
+- Works fine when running locally (without HF banner)
+
+---
+
+## Root Cause Analysis
+
+### Finding 1: SDK Version Mismatch
+
+| Location | Gradio Version |
+|----------|----------------|
+| Local development (`uv pip show gradio`) | **6.0.1** |
+| HuggingFace Spaces (`README.md` frontmatter) | **5.33.0** |
+| Bug fix released in | **5.36** |
+
+**Root Cause:** HuggingFace Spaces is deploying with `sdk_version: "5.33.0"` which is **before** the fix in 5.36.
+
+### Finding 2: Known Gradio Issue
+
+This is a **known issue** reported during the same MCP hackathon:
+
+- **GitHub Issue:** [#11417 - Top of gradio app cut off by huggingface banner](https://github.com/gradio-app/gradio/issues/11417)
+- **Status:** Closed (Fixed)
+- **Fixed in:** Gradio 5.36 via [PR #11427](https://github.com/gradio-app/gradio/pull/11427)
+- **Fix description:** "Rendering of visible components" improvement
+
+### Finding 3: Missing Layout Parameters
+
+Current `app.py` does **not** use recommended layout parameters:
+
+```python
+# Current (problematic):
+with gr.Blocks(title="DeepCritical - Drug Repurposing Research Agent") as demo:
+
+# Recommended:
+with gr.Blocks(title="...", fill_height=True) as demo:
+```
+
+---
+
+## Solution
+
+### Primary Fix: Upgrade SDK Version
+
+Update `README.md` frontmatter:
+
+```yaml
+# Before (broken):
+sdk_version: "5.33.0"
+
+# After (fixed - use 5.36+ or latest 6.x):
+sdk_version: "6.0.1"
+```
+
+### Secondary Fix: Add fill_height Parameter
+
+Update `src/app.py`:
+
+```python
+with gr.Blocks(
+    title="DeepCritical - Drug Repurposing Research Agent",
+    fill_height=True,  # <-- Add this
+) as demo:
+```
+
+### Tertiary Fix: CSS Workaround (if needed)
+
+```python
+css = """
+#chatbot {
+    flex-grow: 1 !important;
+    overflow: auto !important;
+}
+"""
+
+with gr.Blocks(
+    title="...",
+    fill_height=True,
+    css=css,
+) as demo:
+```
+
+---
+
+## References
+
+- [GitHub Issue #11417](https://github.com/gradio-app/gradio/issues/11417) - Original bug report (same hackathon!)
+- [GitHub PR #11427](https://github.com/gradio-app/gradio/pull/11427) - Fix PR
+- [Stack Overflow: Gradio ChatInterface CSS height](https://stackoverflow.com/questions/79084620/how-can-i-adjust-the-height-of-a-gradio-chatinterface-component-using-css)
+- [Stack Overflow: Gradio screen appearance](https://stackoverflow.com/questions/78536986/a-chat-with-gradio-how-to-modify-its-screen-appearance)
+- [GitHub Issue #9923](https://github.com/gradio-app/gradio/issues/9923) - ChatInterface squished in Blocks
+
+---
+
+## Action Items
+
+1. [x] Update `README.md` sdk_version from "5.33.0" to "6.0.1" (or latest) - **DONE**
+2. [x] Add `fill_height=True` to `gr.Blocks()` in `src/app.py` - **DONE**
+3. [x] Run `make check` - 101 tests passed
+4. [ ] Deploy to HuggingFace Spaces and verify fix
+5. [ ] Close GitHub Issue #31 when verified
+
+---
+
+## Investigation Timeline
+
+| Time | Action | Finding |
+|------|--------|---------|
+| 18:52 | Created branch `fix/gradio-ui-scrolling` | - |
+| 18:52 | Web searched "Gradio 2025 ChatInterface top content cut off" | Found Issue #11417 |
+| 18:53 | Fetched Issue #11417 details | Fixed in 5.36 via PR #11427 |
+| 18:53 | Checked local Gradio version | 6.0.1 |
+| 18:54 | Checked README.md sdk_version | **5.33.0** (before fix!) |
+| 18:55 | Confirmed root cause | SDK version mismatch |
+| 19:00 | Updated README.md sdk_version | "5.33.0" → "6.0.1" |
+| 19:00 | Added fill_height=True to app.py | Both fixes applied |
+| 19:02 | Ran `make check` | 101 tests passed |

src/app.py

@@ -183,6 +183,7 @@ def create_demo() -> Any:
     """
     with gr.Blocks(
         title="DeepCritical - Drug Repurposing Research Agent",
+        fill_height=True,
     ) as demo:
         gr.Markdown("""
         # 🧬 DeepCritical