Clarify source staging and refresh model

docs/operating-model.md

@@ -91,3 +91,52 @@ Think of AtoCore as the durable external context hard drive for LLM work:
 - no need to replace the normal project workflow
 
 That is the architecture target.
+
+## Why The Staged Markdown Exists
+
+The staged markdown on Dalidou is a source-input layer, not the end product of
+the system.
+
+In the current deployment model:
+
+1. selected PKM, AtoDrive, or repo docs are copied or mirrored into a Dalidou
+   source path
+2. AtoCore ingests them
+3. the machine store keeps the processed representation
+4. retrieval and context building operate on that machine store
+
+So if the staged docs look very similar to your original PKM notes, that is
+expected. They are source material, not the compiled context layer itself.
+
+## What Happens When A Source Changes
+
+If you edit a PKM note or repo doc at the original source, AtoCore does not
+magically know yet.
+
+The current model is refresh-based:
+
+1. update the human-authoritative source
+2. refresh or re-stage the relevant project source set on Dalidou
+3. run ingestion again
+4. let AtoCore update the machine representation
+
+This is still an intermediate workflow. The long-run target is a cleaner source
+registry and refresh model so that commands like `refresh p05-interferometer`
+become natural and reliable.
+
+## Current Scope Of Ingestion
+
+The current project corpus is intentionally selective, not exhaustive.
+
+For active projects, the goal right now is to ingest:
+
+- high-value anchor docs
+- strong meeting notes with real decisions
+- architecture and constraints docs
+- selected repo context that explains the system shape
+
+The goal is not to dump the entire PKM or whole repo tree into AtoCore on the
+first pass.
+
+So if a project only has some curated notes and not the full project universe in
+the staged area yet, that is normal for the current phase.