[Bug] Plugin nodes not indexed in RefableLookup, causing two-parameter ref() calls to fail

[gaoyuhao000]

Is this a new bug in dbt-core?

• I believe this is a new bug in dbt-core
• I have searched the existing issues, and I could not find an existing issue for this bug

Current Behavior

Bug Location
File: core/dbt/parser/manifest.py (or similar manifest building file)
Method: inject_external_nodes()

The Problem:

• Plugin nodes are correctly added to manifest.nodes via add_node_nofile()
• RefableLookup.populate() only runs once during initial manifest building
• Plugin nodes are injected after RefableLookup is built
• Missing: RefableLookup is never updated with plugin nodes
• Two-parameter ref() calls use RefableLookup exclusively → fail to find plugin nodes

Expected Behavior

Two-parameter ref() syntax should work correctly for plugin-injected models, just like it does for regular dbt package dependencies.

-- This should work without errors
SELECT * FROM {{ ref('external_package', 'external_model') }}

Steps To Reproduce

1. in dbt 1.9 install dbt-loom

# Install dbt-loom (or any plugin that injects models)
pip install dbt-loom

# Configure the plugin
# dbt_loom.config.yml
manifests:
  - name: external_project
    type: file
    config:
      path: /path/to/external/target/manifest.json
    optional: false

2. Create Test Model

-- models/test_plugin_ref.sql
SELECT *
FROM {{ ref('external_project', 'some_external_model') }}

3. Attempt to Parse/Compile
4. Observe the Error

Compilation Error in model test_plugin_ref (models/test_plugin_ref.sql)
Model 'model.your_project.test_plugin_ref' depends on a node named 'external_project' which was not found

5: Verify Single-Parameter Works

-- Change the model to use single-parameter ref
SELECT *
FROM {{ ref('some_external_model') }}

Relevant log output

Environment

dbt-core version: 1.9.4
dbt-loom version: 0.9.1
dbt-snowflake version: 1.9.2
Python version: 3.9.15
OS: macOS 15.6.1

Which database adapter are you using with dbt?

No response

Additional Context

Proposed Fix - add one line to update RefableLookup after injecting plugin nodes:

def inject_external_nodes(self) -> bool:
    # ... existing code ...
    
    pm = plugins.get_plugin_manager(self.root_project.project_name)
    plugin_model_nodes = pm.get_nodes().models
    for node_arg in plugin_model_nodes.values():
        node = ModelNode.from_args(node_arg)
        if (
            node.unique_id not in self.manifest.nodes
            and node.unique_id not in self.manifest.disabled
        ):
            self.manifest.add_node_nofile(node)
            self.manifest.ref_lookup.add_node(node)  # ← ADD THIS LINE
            manifest_nodes_modified = True