feat(skills): add systematic-literature-review skill for multi-paper SLR workflows (#2032)

* feat(skills): add systematic-literature-review skill for multi-paper SLR workflows

Adds a new skill that produces a structured systematic literature review (SLR)
across multiple academic papers on a topic. Addresses #1862 with a pure skill
approach: no new tools, no architectural changes, no new dependencies.

Skill layout:
- SKILL.md — 4+1 phase workflow (plan, search, extract, synthesize, present)
- scripts/arxiv_search.py — arXiv API client, stdlib only, with a
  requests->urllib fallback shim modeled after github-deep-research's
  github_api.py
- templates/{apa,ieee,bibtex}.md — citation format templates selected
  dynamically in Phase 4, mirroring podcast-generation's templates/ pattern

Design notes:
- Multi-paper synthesis uses the existing `task` tool to dispatch extraction
  subagents in parallel. SKILL.md's Phase 3 includes a fixed decision table
  for batch splitting to respect the runtime's MAX_CONCURRENT_SUBAGENTS = 3
  cap, and explicitly tells the agent to strip the "Task Succeeded. Result: "
  prefix before parsing subagent JSON output.
- arXiv only, by design. Semantic Scholar and PubMed adapters would push the
  scope toward a standalone MCP server (see #933) and are intentionally out
  of scope for this skill.
- Coexists with the existing `academic-paper-review` skill: this skill does
  breadth-first synthesis across many papers, academic-paper-review does
  single-paper peer review. The two are routed via distinct triggers and
  can compose (SLR on many + deep review on 1-2 important ones).
- Hard upper bound of 50 papers, tied to the Phase 3 concurrency strategy.
  Larger surveys degrade in synthesis quality and are better split by
  sub-topic.

BibTeX template explicitly uses @misc for arXiv preprints (not @article),
which is the most common mistake when generating BibTeX for arXiv papers.

arxiv_search.py was smoke-tested end-to-end against the live arXiv API with
two query shapes (relevance sort, submittedDate sort with category filter);
all returned JSON fields parse correctly (id normalization, Atom namespace
handling, URL encoding for multi-word queries).

* fix(skills): prevent LLM from saving intermediate search results to file

Adds an explicit "do not save" instruction at the end of Phase 2.
Observed during Test 1 with DeepSeek: the model saved search results
to a markdown file before proceeding to Phase 3, wasting 2-3 tool call
rounds and increasing the risk of hitting the graph recursion limit.
The search JSON should stay in context for Phase 3, not be persisted.

* fix(skills): use relevance+start-date instead of submittedDate sorting

Test 2 revealed that arXiv's submittedDate sorting returns the most
recently submitted papers in the category regardless of query relevance.
Searching "diffusion models" with sortBy=submittedDate in cs.CV returned
papers on spatial memory, Navier-Stokes, and photon-counting CT — none
about diffusion models. The LLM then retried with 4 different queries,
wasting tool calls and approaching the recursion limit.

Fix: always sort by relevance; when the user wants "recent" papers,
combine relevance sorting with --start-date to constrain the time window.
Also add an explicit "run the search exactly once" instruction to prevent
the retry loop.

* fix(skills): wrap multi-word arXiv queries in double quotes for phrase matching

Without quotes, `all:diffusion model` is parsed by arXiv's Lucene as
`all:diffusion OR model`, pulling in unrelated papers from physics
(thermal diffusion) and other fields. Wrapping in double quotes forces
phrase matching: `all:"diffusion model"`.

Also fixes date filtering: the previous bug caused 2011 papers to appear
in results despite --start-date 2024-04-09, because the unquoted query
words were OR'd with the date constraint.

Verified: "diffusion models" --category cs.CV --start-date 2024-04-09
now returns only relevant diffusion model papers published after April
2024.

* fix(skills): add query phrasing guide and enforce subagent delegation

Two fixes from Test 2 observations with DeepSeek:

1. Query phrasing: add a table showing good vs bad query examples.
   The script wraps multi-word queries in double quotes for phrase
   matching, so long queries like "diffusion models in computer vision"
   return 0 results. Guide the LLM to use 2-3 core keywords + --category
   instead.

2. Subagent enforcement: DeepSeek was extracting metadata inline via
   python -c scripts instead of using the task tool. Strengthen Phase 3
   to explicitly name the task tool, say "do not extract metadata
   yourself", and explain why (token budget, isolation). This is more
   direct than the previous natural-language-only approach while still
   providing the reasoning behind the constraint.

* fix(skills): strengthen search keyword guidance and subagent enforcement

Address two issues found during end-to-end testing with DeepSeek:

1. Search retry: LLM passed full topic descriptions as queries (e.g.
   "diffusion models in computer vision"), which returned 0 results due
   to exact phrase matching and triggered retries. Added explicit
   instruction to extract 2-3 core keywords before searching.

2. Subagent bypass: LLM used python -c to extract metadata instead of
   dispatching via task tool. Added explicit prohibition list (python -c,
   bash scripts, inline extraction) with ❌ markers for clarity.

* fix(skills): address Copilot review feedback on SLR skill

- Fix legacy arXiv ID parsing: preserve archive prefix for pre-2007
  papers (e.g. hep-th/9901001 instead of just 9901001)
- Fix phase count: "four phases" -> "five phases"
- Add subagent_enabled prerequisite note to SKILL.md Notes section
- Remove PR-specific references ("PR 1") from ieee.md and bibtex.md
  templates, replace with workflow-scoped wording
- Fix script header: "stdlib only" -> "no additional dependencies
  required", fix relative path to github_api.py reference
- Remove reference to non-existent docs/enhancement/ path in header

* Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

skills/public/systematic-literature-review/templates/ieee.md

@@ -0,0 +1,127 @@
+# IEEE Citation Template
+
+Use this template when the user targets an IEEE conference or journal, or explicitly asks for IEEE format. IEEE uses **numeric citations** — references are numbered in the order they first appear in the text, and in-text citations use bracketed numbers.
+
+## Citation Format Rules
+
+### In-text citations
+
+- **Single reference**: `[1]` — use the number assigned in the References section.
+- **Multiple references**: `[1], [3], [5]` or `[1]–[3]` for consecutive ranges.
+- **Citation as a noun**: "As shown in [1], ..." or "Reference [1] demonstrated...".
+- **Author attribution**: "Vaswani et al. [1] introduced..." — author names are optional in IEEE; use them when it improves readability, always followed by the bracketed number.
+
+Numbers are assigned in **order of first appearance in the text**, not alphabetically. The first reference you cite is `[1]`, the second new reference is `[2]`, and so on.
+
+### Reference list entry for arXiv preprints
+
+IEEE format for arXiv preprints:
+
+```
+[N] A. A. Author, B. B. Author, and C. C. Author, "Title of the paper," arXiv:ARXIV_ID, Year.
+```
+
+**Real example**:
+
+```
+[1] A. Vaswani, N. Shazeer, N. Parmar, J. Uszkoreit, L. Jones, A. N. Gomez, Ł. Kaiser, and I. Polosukhin, "Attention is all you need," arXiv:1706.03762, 2017.
+```
+
+Formatting rules:
+
+- **Author names**: `FirstInitial. LastName` — initials before the last name, opposite of APA. Join with commas; last author gets `and` (no Oxford comma before it in strict IEEE, but accepted).
+- **Title**: in double quotes, sentence case. No italics.
+- **Source**: `arXiv:<id>` — the literal prefix `arXiv:` followed by the bare id (e.g. `arXiv:1706.03762`, not the full URL).
+- **Year**: at the end, after a comma.
+- **URL**: optional in IEEE. Include if the publication venue requires it; otherwise the `arXiv:<id>` identifier is sufficient and is the IEEE-preferred form.
+
+### Special cases
+
+- **More than 6 authors**: IEEE allows listing the first author followed by `et al.`: `A. Vaswani et al., "Attention is all you need," arXiv:1706.03762, 2017.` Use this for papers with many authors to keep reference entries readable.
+- **If the paper has also been published at a venue**: prefer the venue citation format over arXiv. In this workflow we only have arXiv metadata, so always use the arXiv form.
+
+## Report Structure
+
+Follow this structure verbatim. Note that IEEE reports use **numeric citations throughout**, so you need to assign a number to each paper **in order of first appearance** in the Themes section, then use those numbers consistently in per-paper annotations and the reference list.
+
+```markdown
+# Systematic Literature Review: <Topic>
+
+**Date**: <YYYY-MM-DD>
+**Papers surveyed**: <N>
+**Scope**: <arXiv search query, category, time window>
+**Citation format**: IEEE
+
+## Executive Summary
+
+<3-5 sentences summarizing the state of the literature. Cite papers with bracketed numbers as you first introduce them, e.g. "Transformer architectures [1] have become the dominant approach, with extensions focusing on efficiency [2], [3] and long-context handling [4].">
+
+## Methodology
+
+This review surveyed <N> arXiv papers retrieved on <YYYY-MM-DD> using the query `<query>`<, filtered to category <cat>><, published between <start_date> and <end_date>>. Papers were sorted by <relevance | submission date> and the top <N> were included. Metadata extraction was performed by language-model agents, with cross-paper synthesis performed by the lead agent.
+
+**Limitations of this review**: arXiv preprints are not peer-reviewed; coverage is limited to arXiv.
+
+## Themes
+
+<3-6 thematic sections. First appearance of each paper gets a bracketed number; subsequent mentions reuse the same number. The number assignment order is: first paper mentioned in Theme 1 gets [1], next new paper gets [2], etc.>
+
+### Theme 1: <Theme name>
+
+<Paragraphs describing the theme. Cite with bracketed numbers: "The original transformer architecture [1] introduced self-attention, which was later extended in [2] and [3]. Comparative analyses [4] show that...">
+
+### Theme 2: <Theme name>
+
+<...>
+
+## Convergences and Disagreements
+
+**Convergences**: <e.g. "Multiple papers [1], [3], [5] agree that X is necessary.">
+
+**Disagreements**: <e.g. "While [1] argues X, [2] finds the opposite under condition Y.">
+
+## Gaps and Open Questions
+
+<What the collective literature does not yet address, with citations to papers that explicitly mention these gaps.>
+
+## Per-Paper Annotations
+
+<One subsection per paper, ordered by their assigned reference number.>
+
+### [1] Vaswani et al., "Attention is all you need" (2017)
+
+**Research question**: <1 sentence>
+**Methodology**: <1-2 sentences>
+**Key findings**:
+- <bullet>
+- <bullet>
+- <bullet>
+**Limitations**: <1-2 sentences>
+
+### [2] <Next paper>
+
+<...>
+
+## References
+
+<Numbered list in order of first appearance in the text. The number must match the in-text citations above.>
+
+[1] A. Vaswani, N. Shazeer, N. Parmar, J. Uszkoreit, L. Jones, A. N. Gomez, Ł. Kaiser, and I. Polosukhin, "Attention is all you need," arXiv:1706.03762, 2017.
+
+[2] J. Devlin, M.-W. Chang, K. Lee, and K. Toutanova, "BERT: Pre-training of deep bidirectional transformers for language understanding," arXiv:1810.04805, 2018.
+
+<... more entries ...>
+```
+
+## Quality checks before finalizing
+
+Before saving the report, verify:
+
+- [ ] Every paper in the surveyed set has a unique reference number.
+- [ ] Reference numbers are assigned in order of **first appearance in the text**, not alphabetically.
+- [ ] Every bracketed number in the text has a matching entry in the References section.
+- [ ] Every entry in References is cited at least once in the text.
+- [ ] Author names use `FirstInitial. LastName` format (initials before last name).
+- [ ] Titles are in double quotes and sentence case.
+- [ ] arXiv identifiers use the `arXiv:<bare_id>` form, not the full URL.
+- [ ] Per-paper annotations are ordered by reference number, matching the References section order.