refactor(logs): make structured severity automatic

[alongubkin]

Summary

• normalize supported structured application log levels automatically at stdout/stderr capture boundaries
• keep system logs and direct OTLP logs unchanged
• remove the deployment setting from CloudFormation, Helm, runtime environment, and generated core schemas
• retain the original log body and existing fallback behavior

Validation

• cargo check for affected runtime/deployment packages
• 107 CloudFormation generator tests, including rendered template snapshots
• @alienplatform/core build and 93 tests
• generated core and Platform OpenAPI artifacts

[greptile-apps]

Greptile Summary

This PR removes the configurable structured-log parsing setting and makes recognized application severity normalization automatic at stdout/stderr capture boundaries while retaining raw log bodies.

• Removes the log setting from core schemas, deployment environment propagation, CloudFormation, Helm, CLI requests, and generated clients.
• Makes worker-runtime OTLP capture infer application severity unless a record is marked as a system log.
• Makes Kubernetes collector ingestion infer structured severity unconditionally, including for non-application containers currently included by the collector.

Confidence Score: 4/5

The PR should not merge until collector severity normalization is restricted to application logs or the collector preserves and checks an equivalent application/system classification.

The worker-runtime path retains an explicit system marker, but the Kubernetes collector now applies application-level parsing to every collected container record despite ingesting system and sidecar logs without such a marker.

Files Needing Attention: crates/alien-operator/src/collector_logs.rs and crates/alien-helm/src/generator.rs

Important Files Changed

Filename	Overview
crates/alien-core/src/application_logs.rs	Adds a cheap object-shaped input guard while retaining the existing recognized-level parser and conflict behavior.
crates/alien-worker-runtime/src/otlp.rs	Removes the parsing flag and automatically normalizes captured application output while preserving stream severity for explicitly marked system records.
crates/alien-operator/src/collector_logs.rs	Makes severity parsing unconditional even though this collector ingests logs from all namespace-scoped containers without an application/system distinction.
crates/alien-core/src/stack_settings.rs	Removes the obsolete log setting while retaining backward-compatible permissive deserialization of historical unknown fields.
crates/alien-cloudformation/src/generator.rs	Removes the obsolete parameter, condition, metadata, and registration setting from generated templates.
crates/alien-helm/src/generator.rs	Removes the obsolete operator setting, while the existing broad collector input scope exposes the unconditional normalization issue.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  P[Namespace pod logs] --> C[Fluent Bit collector]
  C --> I[/operator /internal/logs/]
  I --> R[CollectorLogRecord]
  R --> S{Recognized JSON level?}
  S -->|Yes| J[Use structured severity]
  S -->|No| F[Use stdout/stderr fallback]
  J --> O[OTLP storage]
  F --> O

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Prompt To Fix All With AI

### Issue 1
crates/alien-operator/src/collector_logs.rs:326-327
**Collector reclassifies system logs**

When a system or sidecar container emits JSON with a recognized level field, the namespace-wide collector now treats that field as application severity instead of retaining the stdout/stderr fallback, causing incorrect severity-based filtering, alerts, and display.

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For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (2): Last reviewed commit: "refactor(logs): make structured severity..." | Re-trigger Greptile}

[greptile-apps]

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