Section Logic Polisher Skill for Codex

Section Logic Polisher (thesis + argument bridges)

Purpose: close the main “paper feel” gap that remains even when a subsection is long and citation-dense:

• missing/weak thesis (paragraph 1 never commits to a claim)
• weak inter-paragraph flow (paragraph islands; no content-bearing bridges)

This is a local, per-H3 polish step that happens after drafting and before merging.

Note: if the main problem is paragraph-count overgrowth, run

paragraph-curator after this check. It only merges adjacent paragraph

boundaries and preserves all prose; semantic redundancy still belongs to the

owning writer.

What this skill blocks on (and what it does not)

Blocking (must fix):

• paragraph 1 lacks an explicit thesis / takeaway (a content claim)

Non-blocking (diagnostic only):

• connector word counts (e.g., “moreover/however/therefore”). Counts are a proxy for paragraph islands, but forcing them as a quota often creates “generator cadence” (paragraph-initial adverbs). Treat these stats as *signals*, not goals.

Role prompt: Logic Editor (argument flow)

You are the logic editor for one survey subsection.

Your job is to make the subsection read like a single argument:
- paragraph 1 commits to a clear thesis (content claim)
- each paragraph has an explicit logical relation to the previous one
- bridges are content-bearing (contrast/causal/implication), not slide narration

Constraints:
- do not add new citations
- do not change citation keys
- do not invent facts

Editing lens:
- if a paragraph does not advance the argument (claim/contrast/eval/limitation), compress or delete it
- if a transition is empty, rewrite it as a content-bearing bridge

Inputs

• sections/ (expects H3 body files like S<sec>_<sub>.md)
• outline/subsection_briefs.jsonl (use thesis + paragraph_plan[].connector_phrase as intent)
• Optional: outline/writer_context_packs.jsonl (preferred; has trimmed anchors/comparisons + must_use)

Outputs

• output/SECTION_LOGIC_REPORT.md (PASS/FAIL for thesis; connector stats shown for diagnosis)

Manual / LLM-first (in place):

• Update the H3 body files under sections/ (e.g., sections/S<sec>_<sub>.md) to fix thesis/bridges (no new citations; keep keys stable)

Workflow (self-loop)

1) Run the checker script to surface the exact failing files.

2) For each failing H3 file:

• Work on the concrete H3 body file (pattern): sections/S<sec>_<sub>.md
• Use outline/subsection_briefs.jsonl as the source of truth for the subsection thesis and paragraph-plan intent.
• If available, prefer outline/writer_context_packs.jsonl to stay aligned with must_use anchors/constraints (no new cites).

• Thesis (blocking)
• Make paragraph 1 end with a conclusion-first thesis sentence.
• Prefer a content claim, not meta narration. Avoid repetitive openers like This subsection argues/surveys ....
• Minimal shape (3 sentences; paraphrase, don’t copy):

1) claim / tension

2) why it matters (protocol/evaluation relevance)

3) how the subsection will resolve it (what contrasts/anchors it will use)

• Flow (fix only when needed)
• Add 1–2 short bridges where paragraphs feel disconnected.
• Prefer subject-first sentences and mid-sentence glue (because/while/which) over paragraph-start adverbs.
• Avoid PPT navigation (Next, we ..., We now turn to ...).

3) Rerun the checker until output/SECTION_LOGIC_REPORT.md is PASS, then

proceed to paragraph-curator, evaluation-anchor-checker, the final

argument-selfloop snapshot, and merge.

Examples

Thesis signal (paragraph 1)

Bad (topic setup only):

• Tool interfaces vary across agent systems, and many recent works explore different designs.

Better (conclusion-first claim):

• A central tension in tool interfaces is balancing expressivity with verifiability; as a result, interface contracts often determine which evaluation claims transfer across environments.

Bad (meta narration):

• This subsection argues that memory is important for agents.

Better (content claim):

• Memory designs trade off retrieval reliability against write-time contamination, and this trade-off shows up as distinct failure modes under fixed evaluation protocols.

Bridges (avoid paragraph islands)

Bad (no relation):

• X does ... (para 2)
• Y does ... (para 3)

Better (explicit tie):

• Whereas X optimizes for <axis>, Y shifts the bottleneck to <axis>; under fixed budgets, this changes whether the reported gains reflect better planning or simply more expensive search.

Done criteria

• output/SECTION_LOGIC_REPORT.md shows - Status: PASS
• No section file contains placeholders (TODO/…/...) or outline meta markers (Intent:/RQ:/Evidence needs:)
• Every H3 has a clear paragraph-1 thesis; bridges are added only where flow is actually broken

Script

Quick Start

• uv run python .codex/skills/section-logic-polisher/scripts/run.py --workspace <workspace>

Notes:

• The script is a checker; it does not rewrite prose.
• Connector stats are printed for diagnosis. Do not “write to the counter”; write to the argument.

All Options

• --workspace <dir>
• --unit-id <U###>
• --inputs <semicolon-separated>
• --outputs <semicolon-separated>
• --checkpoint <C#>

Examples

• Default run:

uv run python .codex/skills/section-logic-polisher/scripts/run.py --workspace <workspace>

• Explicit output path (rare override; prefer defaults):

uv run python .codex/skills/section-logic-polisher/scripts/run.py --workspace <workspace> --outputs output/SECTION_LOGIC_REPORT.md