research

Preamble (run first)

# --- GENERATED PREAMBLE START ---
_PROJECT_ROOT=$(git rev-parse --show-toplevel 2>/dev/null || pwd)
if ! git rev-parse --show-toplevel >/dev/null 2>&1; then
  echo "WARNING: Not inside a git repository. Files will be written to $(pwd)."
fi
mkdir -p ~/.rstack/sessions ~/.rstack/analytics "$_PROJECT_ROOT/.rstack"
touch ~/.rstack/sessions/"$PPID"
find ~/.rstack/sessions -mmin +120 -type f -delete 2>/dev/null || true
_SESSIONS=$(find ~/.rstack/sessions -mmin -120 -type f 2>/dev/null | wc -l | tr -d ' ')
_RSTACK_DIR="$(cd "$(dirname "$0")/.." 2>/dev/null && pwd || echo "$HOME/.claude/skills/rstack")"
_RSTACK_CONFIG="$_RSTACK_DIR/bin/rstack-config"
_UPD=$("$_RSTACK_DIR/bin/rstack-update-check" 2>/dev/null || true)
[ -n "$_UPD" ] && echo "$_UPD" || true
_VENUE=$("$_RSTACK_CONFIG" get venue 2>/dev/null || echo "arxiv")
_COMPUTE=$("$_RSTACK_CONFIG" get compute_preferred 2>/dev/null || echo "modal")
_PROACTIVE=$("$_RSTACK_CONFIG" get proactive 2>/dev/null || echo "true")
_TEL=$("$_RSTACK_CONFIG" get telemetry 2>/dev/null || echo "off")
_TEL_PROMPTED=$([ -f ~/.rstack/.telemetry-prompted ] && echo "yes" || echo "no")
_BRANCH=$(git branch --show-current 2>/dev/null || echo "unknown")
echo "PROJECT_ROOT: $_PROJECT_ROOT"
echo "BRANCH: $_BRANCH"
echo "VENUE: $_VENUE"
echo "COMPUTE: $_COMPUTE"
echo "PROACTIVE: $_PROACTIVE"
if [ ! -f ~/.rstack/.setup-complete ]; then
  echo "NEEDS_SETUP"
fi
_TEL_START=$(date +%s)
_SESSION_ID="$$-$(date +%s)"
echo "TELEMETRY: ${_TEL:-off}"
echo "TEL_PROMPTED: $_TEL_PROMPTED"
if [ "$_TEL" != "off" ]; then
  echo '{"skill":"research","ts":"'$(date -u +%Y-%m-%dT%H:%M:%SZ)'","repo":"'$(basename "$(git rev-parse --show-toplevel 2>/dev/null)" 2>/dev/null || echo "unknown")'"}'  >> ~/.rstack/analytics/skill-usage.jsonl 2>/dev/null || true
fi
if [ "$_TEL" != "off" ]; then
  echo '{"skill":"research","ts":"'$(date -u +%Y-%m-%dT%H:%M:%SZ)'","session_id":"'"$_SESSION_ID"'","rstack_version":"'"$(cat "$_RSTACK_DIR/VERSION" 2>/dev/null | tr -d "[:space:]" || echo "unknown")"'"}'  > ~/.rstack/analytics/.pending-"$_SESSION_ID" 2>/dev/null || true
fi
for _PF in $(find ~/.rstack/analytics -maxdepth 1 -name '.pending-*' 2>/dev/null); do
  if [ -f "$_PF" ]; then
    _PF_BASE="$(basename "$_PF")"
    _PF_SID="${_PF_BASE#.pending-}"
    [ "$_PF_SID" = "$_SESSION_ID" ] && continue
    if [ "$_TEL" != "off" ] && [ -x "$_RSTACK_DIR/bin/rstack-telemetry-log" ]; then
      "$_RSTACK_DIR/bin/rstack-telemetry-log" --event-type skill_run --skill _pending_finalize --outcome unknown --session-id "$_SESSION_ID" 2>/dev/null || true
    fi
    rm -f "$_PF" 2>/dev/null || true
  fi
  break
done
eval "$("$_RSTACK_DIR/bin/rstack-slug" 2>/dev/null)" 2>/dev/null || true
echo "SLUG: ${SLUG:-unknown}"
# --- GENERATED PREAMBLE END ---

If output shows UPGRADE_AVAILABLE <old> <new>: read rstack-upgrade/SKILL.md and follow the "Inline Upgrade Flow". Then continue with this skill. If output shows JUST_UPGRADED <from> <to>: tell user "Running RStack v{to} (just updated!)" and continue.

If output shows NEEDS_SETUP: tell user "RStack not configured. Running /setup first..." Then read setup-skill/SKILL.md and follow it inline.

If TEL_PROMPTED is no: Ask the user about telemetry. Use AskUserQuestion:

Help RStack get better! Community mode shares usage data (which skills you use, how long they take, crash info) with a stable device ID so we can track trends and fix bugs faster. No code, file paths, or repo names are ever sent. Change anytime with rstack-config set telemetry off.

Options:

• A) Help RStack get better! (recommended)
• B) No thanks

If A: run rstack-config set telemetry community

If B: ask a follow-up:

How about anonymous mode? Just a counter that helps us know if anyone's out there.

Options:

• A) Sure, anonymous is fine
• B) No thanks, fully off

If B→A: run rstack-config set telemetry anonymous If B→B: run rstack-config set telemetry off

Always run:

touch ~/.rstack/.telemetry-prompted

This only happens once. If TEL_PROMPTED is yes, skip this entirely.

Important: Note the PROJECT_ROOT value from the preamble output. All file paths below are relative to this project root directory. Work products (idea.md, paper.tex, etc.) go at the project root. Plumbing (.rstack/lit-review.jsonl, .rstack/experiments.jsonl) goes in the .rstack/ subdirectory.

Overview

This is the orchestrator. It chains all RStack skills together with human checkpoints at every phase boundary. The pipeline is NOT linear — every checkpoint allows looping back to earlier phases.

IDEA → /lit-review → /novelty-check → /experiment → /analyze-results → /write-paper → PAPER
  ↑         ↑              ↑               ↑               ↑                ↑
  └─────────┴──────────────┴───────────────┴───────────────┴────────────────┘
                        (revision loops at every checkpoint)

Phase 1: Capture the Idea

Ask the user for their research idea if not provided as an argument.

Save to idea.md at the project root. Create the .rstack/ plumbing directory if it doesn't exist:

_PROJECT_ROOT=$(git rev-parse --show-toplevel 2>/dev/null || pwd)
mkdir -p "$_PROJECT_ROOT/.rstack"

Tell the user: "Starting the full research pipeline. I'll guide you through literature review, novelty assessment, experiments, analysis, and paper writing. You'll have a checkpoint at each phase."

Phase 2: Literature Review

Read the /lit-review skill file at ~/.claude/skills/rstack/lit-review/SKILL.md and follow it inline, skipping its preamble bash block (already run). Note: each subsequent bash block in the sub-skill re-derives _PROJECT_ROOT independently, so those still run normally.

After completion, check: does .rstack/lit-review.jsonl (plumbing) exist and have content?

• If YES: proceed to Phase 3
• If NO (lit-review failed or found nothing): AskUserQuestion — "Literature search found no relevant papers. A) Try different search terms B) Skip lit review and proceed anyway C) Abort"

Phase 3: Novelty Assessment + Idea Refinement

Read the /novelty-check skill file at ~/.claude/skills/rstack/novelty-check/SKILL.md and follow it inline, skipping its preamble.

After completion, check: does refined-idea.md exist at the project root?

• If YES and novelty score >= 4: proceed to Phase 4
• If YES but novelty score < 4: AskUserQuestion — "Novelty score is low ({score}/10). A) Proceed anyway B) Refine the idea C) Pivot to a different angle D) Abort"
• If NO: something went wrong, ask user how to proceed

Revision loop: If user chooses to refine or pivot, update idea.md, optionally re-run /lit-review, then re-run /novelty-check.

Phase 4: Experiments

Read the /experiment skill file at ~/.claude/skills/rstack/experiment/SKILL.md and follow it inline, skipping its preamble.

This phase is iterative. The /experiment skill runs multiple experiment cycles with its own internal checkpoints (every 3 runs by default).

After the user says "stop" or "enough experiments":

• Check: does .rstack/experiments.jsonl (plumbing) have at least one completed run?
• If YES: proceed to Phase 5
• If NO: AskUserQuestion — "No completed experiments. A) Try again B) Provide results manually C) Write paper without experiments (theory paper)"

Revision loop: If results are poor, the user can:

• Change approach → update experiment-plan.md, re-run experiments
• Revise hypothesis → update refined-idea.md, potentially re-run novelty check
• Deepen literature → run additional /lit-review queries

Phase 5: Results Analysis

Read the /analyze-results skill file at ~/.claude/skills/rstack/analyze-results/SKILL.md and follow it inline, skipping its preamble.

After completion, check: do figures exist in analysis/figures/?

• If YES: proceed to Phase 6
• If NO: warn user, proceed to paper writing without figures

Phase 6: Paper Writing

Read the /write-paper skill file at ~/.claude/skills/rstack/write-paper/SKILL.md and follow it inline, skipping its preamble.

After completion, check: does paper.pdf exist at the project root?

• If YES: proceed to Final
• If NO (compilation failed): show error, attempt to fix, retry

Final: Summary

Present the complete research output:

=== RStack Research Complete ===
Idea:        idea.md
Lit Review:  lit-review.md ({N} papers found)
Novelty:     novelty-assessment.md (score: {X}/10)
Experiments: .rstack/experiments.jsonl ({N} runs, best: {metric}={value})
Figures:     analysis/figures/ ({N} figures)
Paper:       paper.pdf ({N} pages)

Work products at project root. Plumbing in .rstack/.

Use AskUserQuestion:

Research pipeline complete. Paper is at paper.pdf.

A) Done — I'm satisfied with the paper B) Revise — go back to a specific phase C) Run more experiments and update the paper

Failure Handling

At each phase transition, if a skill fails:

1. Show the error clearly
2. Offer: Retry / Skip this phase / Abort
3. Never silently continue past a failure
4. Log the failure to ~/.rstack/analytics/skill-usage.jsonl

If the user interrupts at any point, the project state is preserved. They can resume later by running /research again — it will detect existing files and ask where to pick up.

Important Rules

• This skill READS other skill files and follows them inline. It does NOT re-implement their logic.
• Every phase boundary is a human checkpoint. No phase runs without the user's knowledge.
• State is always written to disk before checkpoints, so nothing is lost if the session ends.
• The pipeline supports any entry point: if .rstack/lit-review.jsonl (plumbing) already exists, skip Phase 2 and ask user if they want to re-run it or proceed.

Telemetry (run last)

After the skill workflow completes (success, error, or abort), log the telemetry event.

# --- GENERATED EPILOGUE START ---
_TEL_END=$(date +%s)
_TEL_DUR=$(( _TEL_END - _TEL_START ))
rm -f ~/.rstack/analytics/.pending-"$_SESSION_ID" 2>/dev/null || true
if [ "$_TEL" != "off" ]; then
  echo '{"skill":"research","duration_s":"'"$_TEL_DUR"'","outcome":"OUTCOME","session":"'"$_SESSION_ID"'","ts":"'$(date -u +%Y-%m-%dT%H:%M:%SZ)'"}' >> ~/.rstack/analytics/skill-usage.jsonl 2>/dev/null || true
fi
if [ "$_TEL" != "off" ] && [ -x "$_RSTACK_DIR/bin/rstack-telemetry-log" ]; then
  "$_RSTACK_DIR/bin/rstack-telemetry-log" \
    --skill "research" --duration "$_TEL_DUR" --outcome "OUTCOME" \
    --session-id "$_SESSION_ID" --pipeline-stage "research" --venue "$_VENUE" 2>/dev/null &
fi
# --- GENERATED EPILOGUE END ---

Replace OUTCOME with success/error/abort based on the workflow result.