fix(refacto-p2): more standardize

[aeppling]

Summary

• constant extract of repetitive patterns
• more covering for run_filtered wrapper and sub wrappers for specifics cmds environments
• automod for cmds environments (auto discover)
• merge pattern & rules for routing

Test plan

• all test pass
• all edge cases kept (exclusions not covered by global wrappers)

[FlorianBruniaux]

Three things to fix before merging.

1. Silent JSON fallback in container.rs (run_kubectl_json)
When serde_json::from_str fails, the closure returns stdout.to_string() with no warning. Users get raw kubectl JSON (potentially thousands of tokens) with no indication the filter failed. Add eprintln!("[rtk] kubectl: JSON parse failed: {}", e) in the Err branch.

2. Savings inflation in runner.rs (filter_stdout_only path)
When filter_stdout_only is true, text_to_filter = &stdout but timer.track() is called with &raw (stdout + stderr combined) as the input. Savings % gets inflated by stderr length. On noisy commands like docker build, stderr can be substantial. The fix: track &stdout as raw input when filter_stdout_only is true. This is pre-existing but it is now centralized in one place, so the right time to fix it is here.

3. automod contributor contract change
Every .rs file dropped into src/cmds/system/ is now automatically a public module. The previous pub mod foo; declarations were a forcing function. A developer who adds a WIP file directly into the directory will silently expose it. Low risk, but worth a comment or a note in the README explaining that automod is in use.

The run_aws_filtered deduplication (180 lines to 60) and the run_passthrough centralization are both good. Depends on #904, merge that first.

[aeppling]

Rebased with refacto-folders-and-documentation and review issues resolved @FlorianBruniaux