[proton0210]

Closes #4749.

E3004 previously removed SAM edges only after discovering a cycle. That reported the non-SAM portion of false cycles and hid real cycles through SAM resources. Build a separate dependency graph before cycle detection, retaining dependencies of underlying CloudFormation resources and generated execution roles, and excluding properties belonging to separate generated stages, events and deployment preferences.

Cover the three reported templates, independent native cycles, execution-role policies, explicit roles with unused policies, and Ref/GetAtt/Sub/DependsOn self-dependencies. The original graph and template remain available unchanged to other rules.

This remains conservative for dependencies contributed solely by generated event resources; it does not restore the full SAM transform or add a translator dependency.

Validation: 15 focused tests passed, alongside the full unit suite. Three audit passes covered original-source reproduction, non-regression and edge-case checks, and final combined review (3,027 unit/integration tests passed plus the separate schema-updater test; four data tests retain the default exclusion).

[codecov]

Codecov Report

❌ Patch coverage is 91.17647% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.67%. Comparing base (7fbb68c) to head (44eb695).

Files with missing lines	Patch %	Lines
src/cfnlint/rules/resources/CircularDependency.py	91.17%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4755      +/-   ##
==========================================
- Coverage   94.68%   94.67%   -0.01%     
==========================================
  Files         439      439              
  Lines       15910    15939      +29     
  Branches     3079     3085       +6     
==========================================
+ Hits        15065    15091      +26     
- Misses        463      465       +2     
- Partials      382      383       +1     

Flag	Coverage Δ
unittests	94.67% <91.17%> (-0.01%)	⬇️

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