feat: Update documentation and configuration for onboarding, graph defaults, and workspace navigation

knowledge/obsidian-usage.md

@@ -75,6 +75,35 @@ If a node is isolated, it may still be valid. It may be:
 
 ---
 
+## Global Graph Defaults
+
+The global graph is configured for onboarding and project navigation, not full filesystem inspection.
+
+It intentionally hides generic technical filenames such as:
+
+- `index`
+- `README`
+- `AGENTS`
+- `SKILL`
+
+Those files still exist and remain valid workspace files. They are hidden from the graph because Obsidian displays only the basename, which creates many indistinguishable nodes.
+
+Use the file explorer or search when you need a specific technical file. Use the graph when you want to understand relationships between project concepts.
+
+---
+
+## When To Show Technical Files
+
+Temporarily remove these filters from the graph search when debugging workspace internals:
+
+```text
+-file:index -file:README -file:AGENTS -file:SKILL
+```
+
+For normal onboarding, keep them hidden and navigate through the named maps.
+
+---
+
 ## Editing Rules
 
 - Edit canonical memory files when the fact is clear.