Misnamed Key in analysis.json out: Remove `system_dependency_graph` from the output and save only the `call_graph`

[rahlk]

Describe the bug
The output file analysis.json currently contains a key named system_dependency_graph which is a misnomer and does not accurately reflect the data it contains.

To Reproduce
Steps to reproduce the behavior:

1. Run the analysis tool on any codebase
2. Examine the resulting analysis.json file
3. Note that it contains both system_dependency_graph and call_graph keys

Expected behavior
The analysis.json file should only contain the key call_graph since that accurately describes the data. The system_dependency_graph key should be removed as it's misleadingly named.

Additional context
The current naming creates confusion for users who expect the system_dependency_graph to represent something different than what it actually contains. This appears to be a legacy naming issue that should be resolved by standardizing on the more accurate call_graph terminology.