Auto layout to Manual Layout removes nested subgraphs

[pyousefi]

Describe the bug

---
config:
  layout: dagre
---
flowchart LR
 subgraph s1["scrm-databricks"]
    direction TB
        db_etl["ETL build Supply Chain Master Data"]
        db_pg_jobs["Postgres<br>population jobs"]
        db_neo4j_jobs["Neo4j population<br>jobs ¹"]
  end
 subgraph s2["scrm-postgres"]
        ddl["scrm_io schema<br>DDL"]
  end
 subgraph ado["ADO Repos: Single Branch; Manual Deploy)"]
        s1
        s2
  end
 subgraph databricks["Databricks"]
        genpro["Genpro<br>Gold Layer"]
        scmd["Supply Chain Master Data (scrm_io)"]
  end
 subgraph postgres["postgres"]
        pg["scrm_io"]
  end
 subgraph neo4j["neo4j graph db"]
        n4j["scrm_db"]
  end
 subgraph s3["Data Tier"]
        databricks
        postgres
        neo4j
  end
 subgraph api["scrm-api"]
        django["Django API<br>reads Postgres"]
  end
 subgraph ui["scrm-ui"]
        frontend["Frontend"]
  end
 subgraph infra["Infrastructure"]
        iac["scrm-iac<br>Terraform"]
        k8s["scrm-k8s-config<br>K8s manifests"]
  end
 subgraph github["App Layer — GitHub Repos (Branch Promotion)"]
        api
        ui
        infra
  end
  
    scmd --> genpro
    genpro <-- read / write --> db_etl
    db_etl -- write --> scmd
    ddl -- migrations --> pg
    db_etl --> db_pg_jobs & db_neo4j_jobs
    db_pg_jobs -- populates --> pg
    db_neo4j_jobs -- builds & populates --> n4j
    pg -- reads --> django
    django -- serves --> frontend
    iac -. provisions .-> api & ui
    k8s -. deploys .-> api & ui

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To Reproduce
Steps to reproduce the behavior:

1. Go to 'Chart'
2. Add the above code for an Auto Layout
3. Convert to Manual Layout
4. See un-encapsulation of subgraphs

Expected behavior
Maintain encapsulated subgraphs

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Tahoe 26.2
• Browser: Chrome Version 145.0.7632.77 (Official Build) (arm64)

Additional context
Add any other context about the problem here.

[rajat-ht]

Hi @pyousefi

We’re able to reproduce the issue where nested subgraphs lose encapsulation when switching from Auto Layout to Manual Layout. I’ve logged this internally, and the team will investigate.

We’ll update the issue once we have progress. Thanks again for flagging this.