Update schema documentation for removed included_file_schema and remove deprecated safe-jobs field

[Copilot]

included_file_schema.json was removed but documentation still referenced it across 4 files. Additionally, safe-jobs implementation details were undocumented, creating confusion about whether it's a user-facing field. The deprecated top-level SafeJobs field has been removed from the Go code to align with the schema.

Changes

Removed stale schema references:

• specs/schema-validation.md - Updated from 3 to 2 schemas, removed go:embed example
• skills/developer/SKILL.md - Removed from schema files table
• .github/workflows/schema-consistency-checker.md - Removed from analysis files list
• .github/workflows/schema-consistency-checker.lock.yml - Recompiled to reflect markdown changes

Clarified safe-jobs implementation:

• Added note in docs/src/content/docs/reference/safe-outputs.md explaining safe-jobs is internal-only, accessed via safe-outputs.jobs: configuration
• Updated schema consistency checker to annotate pkg/workflow/safe_jobs.go as internal implementation

Removed deprecated safe-jobs field:

• Removed deprecated SafeJobs field from FrontmatterConfig struct in pkg/workflow/frontmatter_types.go
• Removed related serialization code in ToMap() method
• Updated test to use safe-outputs.jobs instead of deprecated safe-jobs syntax

Context

Users configure custom safe output jobs via safe-outputs.jobs: in frontmatter. The compiler internally processes these as "safe-jobs" (pkg/workflow/safe_jobs.go), but the top-level safe-jobs: key is deprecated and rejected by schema validation. The Go code now aligns with the schema by removing the deprecated field, preventing configuration errors and enforcing the correct pattern.

Original prompt

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This section details on the original issue you should resolve

<issue_title>[deep-report] Update schema documentation for removed included_file_schema and safe-jobs guidance</issue_title>
<issue_description>### Description
Schema consistency analysis reports that included_file_schema.json has been removed but multiple docs still reference it, and safe-jobs is accessed in code but missing from the schema and frontmatter reference. Update the affected docs and clarify whether safe-jobs is internal-only or user-facing, aligning schema and documentation.

Expected Impact

Reduce developer confusion and prevent schema/documentation drift that causes invalid configurations or misunderstanding.

Suggested Agent

Schema Consistency Checker agent

Estimated Effort

Quick (< 1 hour)

Data Source

DeepReport Intelligence Briefing 2026-01-22; schema consistency discussion #11121.

AI generated by DeepReport - Intelligence Gathering Agent

Comments on the Issue (you are @copilot in this section)

• Fixes [deep-report] Update schema documentation for removed included_file_schema and safe-jobs guidance #11328

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[pelikhan]

@copilot remove deprecated top level safe-jobs from schema.

[Copilot]

@copilot remove deprecated top level safe-jobs from schema.

Done. Removed the deprecated SafeJobs field from FrontmatterConfig struct in pkg/workflow/frontmatter_types.go and updated the test to use safe-outputs.jobs instead. The schema already correctly rejects top-level safe-jobs: syntax. (08aad02)