update docs

Author: y9c

docs/getting-started.md

@@ -250,7 +250,7 @@ metagene.plot_profile(gene_bins, gene_splits, "custom_analysis.png")
 
 ## Next Steps
 
-- 📖 **[API Reference]({{ site.baseurl }}{% link api-reference.md %})**: Detailed function documentation
-- 🎨 **[Plotting Guide]({{ site.baseurl }}{% link plotting.md %})**: Customizing your visualizations
-- 🔧 **[Advanced Usage]({{ site.baseurl }}{% link advanced.md %})**: Power user features
-- 💡 **[Examples]({{ site.baseurl }}{% link examples.md %})**: More complete workflows
+- 📖 **[API Reference](api-reference.md)**: Detailed function documentation
+- 🎨 **[Plotting Guide](plotting.md)**: Customizing your visualizations
+- 🔧 **[Advanced Usage](advanced.md)**: Power user features
+- 💡 **[Examples](examples.md)**: More complete workflows

docs/index.md

@@ -12,7 +12,7 @@ permalink: /
 A powerful Python package for metagene profiling analysis and visualization, featuring automatic reference downloading, rich CLI interface, and comprehensive plotting capabilities.
 {: .fs-6 .fw-300 }
 
-[Get started now]({{ site.baseurl }}{% link getting-started.md %}){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
+[Get started now](getting-started.md){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
 [View it on GitHub](https://github.com/y9c/metagene){: .btn .fs-5 .mb-4 .mb-md-0 }
 
 ---
@@ -102,6 +102,6 @@ Metagene analysis is a powerful technique for visualizing the distribution of ge
 
 ## Getting Help
 
-- 📖 **[Documentation]({{ site.baseurl }}{% link getting-started.md %})**: Complete guides and API reference
+- 📖 **[Documentation](getting-started.md)**: Complete guides and API reference
 - 🐛 **[Issues](https://github.com/y9c/metagene/issues)**: Report bugs or request features
 - 💬 **[Discussions](https://github.com/y9c/metagene/discussions)**: Ask questions and share ideas