diff --git a/dev/big_viewport.html b/dev/big_viewport.html
index 77df754d..60130da5 100644
--- a/dev/big_viewport.html
+++ b/dev/big_viewport.html
@@ -52,7 +52,7 @@
"width": 1000,
"height": 1000,
"url": "https://www.encodeproject.org/files/ENCFF799QGA/@@download/ENCFF799QGA.hic",
- "name": "in-situ agar GM12878 MboI experiment",
+ // "name": "in-situ agar GM12878 MboI experiment",
"tracks": [
{
"url": "https://www.dropbox.com/s/gvfvcvt146rtm5b/GSE63525_GM12878_subcompartments.bed?dl=0",
diff --git a/dev/dat-sequence-gene-track.html b/dev/dat-sequence-gene-track.html
index d25495de..fcd01143 100644
--- a/dev/dat-sequence-gene-track.html
+++ b/dev/dat-sequence-gene-track.html
@@ -61,7 +61,7 @@
],
}
- juicebox.init(document.getElementById("app-container"), config_deep_map)
+ juicebox.init(document.getElementById("app-container"), config)
.then(browser => {
console.log(`${ browser.id } is good to go`)
diff --git a/docs/EXTERNAL_PROJECT_INTEGRATION.md b/docs/EXTERNAL_PROJECT_INTEGRATION.md
new file mode 100644
index 00000000..c5c96f65
--- /dev/null
+++ b/docs/EXTERNAL_PROJECT_INTEGRATION.md
@@ -0,0 +1,159 @@
+# Integrating External Projects with Juicebox.js
+
+This document describes how to work with external projects (like Spacewalk) that use Juicebox.js.
+
+## Multi-Root Workspace (Current Approach)
+
+**We use a multi-root workspace to reference Spacewalk without copying files.**
+
+### Setup:
+1. Ensure Spacewalk is cloned locally (e.g., as a sibling directory: `../spacewalk`)
+2. Open `juicebox-with-spacewalk.code-workspace` in Cursor/VS Code
+3. Both projects will appear in the file explorer side-by-side
+
+### Benefits:
+- ✅ Full code navigation and IntelliSense across both projects
+- ✅ Can search across both codebases
+- ✅ No file duplication
+- ✅ Always sees latest Spacewalk changes immediately
+- ✅ Git history stays separate
+- ✅ Cursor AI can understand both codebases together
+
+### Usage:
+```bash
+# Open the workspace file in Cursor
+cursor juicebox-with-spacewalk.code-workspace
+
+# Or in VS Code
+code juicebox-with-spacewalk.code-workspace
+```
+
+### Updating the Spacewalk Path:
+If your Spacewalk repository is in a different location, edit `juicebox-with-spacewalk.code-workspace` and update the path:
+```json
+{
+ "name": "Spacewalk (External Reference)",
+ "path": "/absolute/path/to/spacewalk" // or "../relative/path/to/spacewalk"
+}
+```
+
+## Option 2: Git Submodules
+
+**Best for:** When Spacewalk is a separate Git repository
+
+### Setup:
+```bash
+# Add Spacewalk as a submodule
+git submodule add spacewalk-reference
+
+# Or if Spacewalk is already a submodule elsewhere
+git submodule add external/spacewalk
+```
+
+### Benefits:
+- ✅ Tracks specific commit of Spacewalk
+- ✅ Can update to latest version easily
+- ✅ Keeps projects separate
+- ✅ Works well with CI/CD
+
+### Drawbacks:
+- ⚠️ Requires submodule initialization (`git submodule update --init`)
+- ⚠️ Can be confusing for team members
+
+## Option 3: Symbolic Links
+
+**Best for:** Quick local development (not recommended for Git)
+
+### Setup:
+```bash
+# Create a symlink to Spacewalk's juiceboxPanel.js
+ln -s /path/to/spacewalk/src/panels/juiceboxPanel.js spacewalk-code/juiceboxPanel.js
+```
+
+### Benefits:
+- ✅ Always points to latest version
+- ✅ No duplication
+
+### Drawbacks:
+- ⚠️ Symlinks don't work well in Git (platform-specific)
+- ⚠️ Can break if Spacewalk moves
+- ⚠️ Not portable across machines
+
+## Option 4: npm/yarn Workspaces (If Both Are Packages)
+
+**Best for:** When both projects are npm packages
+
+### Setup:
+Create a root `package.json`:
+```json
+{
+ "name": "juicebox-workspace",
+ "private": true,
+ "workspaces": [
+ ".",
+ "../spacewalk"
+ ]
+}
+```
+
+### Benefits:
+- ✅ Shared dependencies
+- ✅ Can link packages locally
+- ✅ Standard npm workflow
+
+## Option 5: GitHub Integration
+
+**Best for:** Reference code from GitHub without cloning
+
+### Using GitHub CLI:
+```bash
+# View file from GitHub repo
+gh repo view /spacewalk --web
+
+# Or use GitHub's web interface to browse
+```
+
+### Using Cursor's GitHub Integration:
+- Cursor can reference GitHub repos in some contexts
+- Use GitHub URLs in comments/links
+- Not as seamless as local files
+
+## Option 6: Documentation-Based Approach
+
+**Best for:** When you just need to document usage patterns
+
+### Create a reference file:
+```markdown
+# Spacewalk Integration Reference
+
+See: https://github.com/your-org/spacewalk/blob/main/src/panels/juiceboxPanel.js
+
+Key integration points:
+- Line 82: `hic.restoreSession()`
+- Line 89: `hic.getCurrentBrowser()`
+- etc.
+```
+
+## Current Setup
+
+We use the **Multi-Root Workspace** approach. The workspace file (`juicebox-with-spacewalk.code-workspace`) includes both:
+- The juicebox.js project (current directory)
+- The Spacewalk project (external reference)
+
+This allows Cursor to understand both codebases together, making it easy to:
+- Check compatibility when refactoring Juicebox.js
+- See how Spacewalk uses Juicebox.js APIs
+- Navigate between both projects seamlessly
+- Get IntelliSense and code completion across both
+
+### Notes:
+- The workspace file is committed to Git, but Spacewalk itself is not
+- Each developer needs to have Spacewalk cloned locally
+- Update the path in the workspace file if Spacewalk is in a different location
+
+## Questions?
+
+- For workspace setup: See Cursor/VS Code documentation on multi-root workspaces
+- For Git submodules: See `git help submodule`
+- For npm workspaces: See npm/yarn workspace documentation
+
diff --git a/examples/juicebox-api.html b/examples/juicebox-api.html
index dd11dcb8..9111a19d 100644
--- a/examples/juicebox-api.html
+++ b/examples/juicebox-api.html
@@ -10,7 +10,7 @@
-
+
diff --git a/examples/juicebox-minimal.html b/examples/juicebox-minimal.html
index 8626591b..d571a2e3 100644
--- a/examples/juicebox-minimal.html
+++ b/examples/juicebox-minimal.html
@@ -9,7 +9,7 @@
-
+
@@ -19,18 +19,15 @@
diff --git a/examples/juicebox.html b/examples/juicebox.html
index df47ba6e..c990fd9a 100644
--- a/examples/juicebox.html
+++ b/examples/juicebox.html
@@ -9,7 +9,7 @@
-
+
@@ -19,7 +19,7 @@