thesis-markdown-aligner

Thesis Markdown Aligner

Triggers & routing

• Trigger: markdown alignment, thesis markdown align, terminology unification, symbol unification, metric unification, chapter merging.
• Use when: Each chapter has been initially restructured, but the entire thesis still has terminology drift, inconsistent metric conventions, chaotic chapter boundaries, or looks like multiple papers pieced together.
• Skip if: The roles of the chapters have not yet been determined, or currently only one chapter is being revised locally.
• Network: none.
• Guardrail: Do not write back to tex here; first converge the intermediate layer, then enter the delivery layer.

Inputs

• Restructured chapter Markdown
• codex_md/question_list.md

Outputs

• codex_md/00_thesis_outline.md
• codex_md/terminology_glossary.md
• codex_md/symbol_metric_table.md
• Evidence gap list (can be merged into missing_info.md or a separate file)

Load Order

Always read:

• references/overview.md
• references/alignment_axes.md

Machine-readable contract:

• assets/markdown_alignment_contract.json

Workflow

1. Unify the main thread and chapter boundaries
2. Unify terminology, abbreviations, symbols, and metrics
3. Identify duplicate content and content that should be moved up or down
4. Mark evidence gaps that have not yet been closed

Key Rule

If the chapters cannot yet share the same set of terminology, symbols, and metric conventions, do not enter tex-writeback。