Hello again,
I've been testing tree-sitter-stack-graphs-python via the cli, and while I have great results on a single file, I was not able to obtain concluent output on multiple files with modules.

Here is a minimal reproduction of my issue:

Given the following directory structure (working dir being: /Users/nohehf/tmp/py):

.
├── main.py
└── module.py

With:

# main.py
import module

baz = module.foo

# module.py
foo = "bar"

If I run:

DIR="/Users/nohehf/tmp/py"

tree-sitter-stack-graphs-python clean --all
tree-sitter-stack-graphs-python index $DIR
tree-sitter-stack-graphs-python status $DIR
tree-sitter-stack-graphs-python visualize $DIR

I get:

/Users/nohehf/tmp/py/main.py: indexed
/Users/nohehf/tmp/py/module.py: indexed
Visualization at stack-graph.html

Now if I query main.py on the foo reference (main.py:3:14), it does not find the definition in module.py:

tree-sitter-stack-graphs-python query definition "main.py:3:14"

/Users/nohehf/tmp/py/main.py:3:14: found 0 definitions for 1 references
queried reference
/Users/nohehf/tmp/py/main.py:3:14:
3 | baz = module.foo
  |              ^^^

has no definitions

However, trying to reproduce the behaviour in a test (test.py) I get no issues:

#------ path: module.py ------#

foo = "bar"

#------ path: main.py ------#

import module

baz = module.foo
#            ^ defined: 3

tree-sitter-stack-graphs-python test test.py
test.py: success

Am I missing something with the cli ? Are tests really behaving like those are separate files ?

I'm sure this is supposed to work and I have trouble understanding what's going on in the graph visualization:

Thank you