Refresh research

Research Refresh Protocol

Overview

Re-fetch live research sources (repos, docs), detect meaningful changes since initial capture, and update synthesis files. Raw sources are versioned (never overwritten), syntheses are surgically updated, and INDEX.md is rebuilt.

Core principles:

1. Only refreshable sources are fetched. repo and docs source types. Blogs, papers, videos, and internal docs are static — skip them.
2. Raw sources are versioned, never overwritten. New fetch → new file with today's date.
3. Syntheses are updated, not replaced. Preserve analysis and structure; update facts.

When to Use

User types /refresh-research followed by:

Invocation	Behavior
(empty)	Interactive — show stale entries, let user pick which to refresh
research/agent-memory/cognee-architecture.md	Refresh a specific synthesis file
agent-memory	All refreshable entries in that category
--all	All refreshable entries across all categories
--stale 14	Entries not checked in 14+ days (default threshold: 30)
--backfill	One-time: add source_type to entries missing it
--audit	Dry-run: staleness report, no modifications

Flags can be combined: /refresh-research agent-memory --stale 7

Frontmatter Fields

Three optional fields extend the existing synthesis frontmatter:

---
tags: [github, memory, open-source]
date: 2026-02-12              # original research date (unchanged meaning)
source: https://docs.cognee.ai/
source_type: docs              # NEW — repo | docs | blog | paper | internal | video
last_checked: 2026-03-16      # NEW — when last verified against source
refresh_status: changed        # NEW — changed | unchanged | dead-link | archived
---

• source_type gates refresh eligibility — only repo and docs are refreshable
• last_checked is the staleness clock (separate from date which means "first captured")
• refresh_status is informational only (doesn't gate behavior)

Source Type Classification Logic

When source_type is missing, auto-detect from the source URL:

github.com/{owner}/{repo}                  → repo
contains "docs." or "/docs" or "/api"      → docs
contains ".io" or ".dev" or ".ai"          → docs (if not a blog path)
contains "blog" or "medium" or "substack"  → blog
contains "arxiv" or ".pdf"                 → paper
starts with "internal" or empty            → internal
contains "youtube" or "youtu.be"           → video
else                                       → blog (safe default, not refreshable)

Borderline cases: flag for user confirmation during --backfill.

Workflow (MANDATORY — 8 Steps)

You MUST follow this order. No skipping steps.

---

Step 0: Build Candidate List

Based on invocation mode:

1. Specific file: Read that file's frontmatter. If missing source_type, auto-detect from URL.
2. Category: Scan all research/{category}/*.md files.
3. --all: Scan all research/**/*.md files (excluding INDEX.md, README.md, etc.).
4. --stale N: Scan all, then filter to entries where last_checked is missing or older than N days (default 30).
5. Empty (interactive): Scan all, display staleness table, ask user which to refresh.
6. --backfill: Jump to Backfill Mode (see below).
7. --audit: Jump to Audit Mode (see below).

Filter to refreshable types: Only proceed with entries where source_type is repo or docs (auto-detect if missing).

Display staleness table:

Refreshable entries:
| # | File | Source Type | Last Checked | Days Stale | Status |
|---|------|-------------|-------------|------------|--------|
| 1 | research/agent-memory/cognee-architecture.md | docs | (never) | 33+ | — |
| 2 | research/tools/ntfy.md | docs | 2026-03-11 | 5 | unchanged |
...

N entries eligible for refresh. Proceed with all / pick numbers / cancel?

Confirm with user before proceeding. Never auto-refresh without confirmation.

---

Step 1: Fetch Current Content

For each confirmed entry:

For repo source type:

1. Extract {owner}/{repo} from the source URL
2. Fast-path check: gh api repos/{owner}/{repo} --jq '.pushed_at'
   • Compare pushed_at with last_checked
   • If no pushes since last check → mark unchanged, update last_checked, skip
3. If changed: fetch key content
   • gh api repos/{owner}/{repo}/git/trees/HEAD?recursive=1 --jq '[.tree[] | select(.type=="blob") | .path]'
   • Identify README, docs/, key .md files (same logic as /research Step 1)
   • Fetch each via gh api repos/{owner}/{repo}/contents/{path} --jq '.content' | tr -d '\n' | base64 -d
   • Also fetch: gh api repos/{owner}/{repo}/releases?per_page=5 for recent releases

For docs source type:

1. Try Context7 first:
   • resolve-library-id with the library/tool name
   • If resolved: query-docs for key topics
2. If Context7 has no coverage: fall back to WebFetch on the source URL
3. If 404 or unreachable: mark refresh_status: dead-link, update last_checked, report to user, skip

Error handling:

• 404 / dead link → mark dead-link, preserve synthesis, report
• Repo archived → mark archived, note in Update Log
• GitHub rate limit → gh api rate_limit, report quota, offer to continue or stop

---

Step 2: Change Detection

For each fetched entry:

1. Load existing raw source from resources/ (find the most recent file matching the topic)

2. Structural diff — compare:

   • Section headers (H1-H4)
   • Version numbers (semver patterns)
   • Key content blocks (feature lists, API endpoints, architecture sections)
   • For repos: star count, last commit date, release versions

3. Classify the change:

   • No changes → mark unchanged, update last_checked only, skip Steps 3-6
   • Minor update → version bump, small section additions, typo fixes
   • Major update → new features, architecture changes, breaking changes, significant new content

4. Report diff summary to user:

## cognee-architecture.md
Source: https://docs.cognee.ai/
Change level: MINOR
- Version bump: 0.5.0 → 0.6.2
- New section: "Streaming Pipeline"
- Updated: "Storage Architecture" (minor wording changes)

Proceed with update? [y/n/skip]

Wait for user confirmation before modifying any files.

---

Step 3: Save New Raw Source (Versioned)

Write fetched content to resources/ with today's date:

• Format: resources/[topic]-[type]-YYYY-MM-DD.md
• Examples:
  • resources/cognee-docs-2026-03-16.md
  • resources/ntfy-readme-2026-03-16.md

Rules:

• Old raw files are NEVER deleted or overwritten
• Use the same [topic] slug as the original raw source file
• Include a header comment: <!-- Refresh fetch: YYYY-MM-DD, previous: resources/[old-filename] -->

Verify file exists before continuing: ls resources/[filename]

---

Step 4: Update Synthesis

Based on change classification:

Minor changes:

• Surgical section updates — find the specific section, update in place
• Version number bumps in overview/header
• Add new subsections where content was added upstream
• Do NOT rewrite existing analysis paragraphs

Major changes:

• Re-synthesize using existing structure as scaffolding
• Preserve: analysis, opinions, cross-references, Bridge to Technical Work
• Update: facts, feature lists, architecture descriptions, version info
• Add new sections for genuinely new content

Always add an Update Log entry (before the References section):

### Update Log

- **2026-03-16:** Refreshed from source. Version 0.5.0 → 0.6.2. Added Streaming Pipeline section. Updated storage architecture details. ([raw source](resources/cognee-docs-2026-03-16.md))

If an ### Update Log section already exists, append to it.

Update frontmatter:

last_checked: 2026-03-16  # update to today
refresh_status: changed   # set to changed

Leave date unchanged — it records when the topic was first researched, not when it was last refreshed.

Keep source and tags unchanged unless the refresh reveals new relevant tags.

---

Step 5: Update References Section

Add the new raw source file to the ## References → ### Raw Sources list:

- `resources/cognee-docs-2026-03-16.md` — Refresh fetch: updated docs content, 2026-03-16

Do NOT remove existing raw source entries — they form the version history.

---

Step 6: Cross-Reference Check (Lightweight)

Only for major changes:

1. Search research/INDEX.md and research/**/*.md for references to the updated entry
2. Check if any related syntheses cite outdated facts that this refresh corrected
3. Do NOT auto-modify related files — just flag for user review:

Cross-reference alert:
- research/agent-memory/tool-comparison.md references Cognee v0.5.0
  → Cognee is now v0.6.2, comparison may need updating

Skip this step entirely for minor changes.

---

Step 7: Rebuild INDEX.md

python3 "${CLAUDE_PLUGIN_ROOT}/scripts/rebuild-research-index.py"

Run from the project root. Expected output: Rebuilt INDEX.md: N entries

If the script fails, manually update the row in research/INDEX.md for the refreshed entry.

Do NOT skip this step. It is the final required action.

---

Backfill Mode (--backfill)

One-time migration: add source_type to entries missing it.

1. Scan all research/**/*.md files
2. For each file missing source_type in frontmatter: a. Read the source field b. Auto-classify using the Source Type Classification Logic above c. Display classification for user review:

   Backfill classifications:
   | File | Source URL | Detected Type | Confidence |
   |------|-----------|---------------|------------|
   | cognee-architecture.md | https://docs.cognee.ai/ | docs | high |
   | rowboat.md | https://github.com/rowboatlabs/rowboat | repo | high |
   | agent-memory-landscape-analysis.md | (none) | internal | high |
   | ai-routing-quick-reference.md | (none) | internal | high |
   ...
   

   d. Flag borderline cases (confidence: low) for user confirmation e. After user confirms, write source_type into each file's frontmatter
3. Rebuild INDEX.md: python3 "${CLAUDE_PLUGIN_ROOT}/scripts/rebuild-research-index.py"

Backfill does NOT refresh content — it only adds the source_type field.

---

Audit Mode (--audit)

Dry-run staleness report. No files are modified.

1. Scan all research/**/*.md files
2. Classify each by source_type (auto-detect if missing)
3. Calculate staleness from last_checked (or date if last_checked is missing)
4. Output report:

# Research Freshness Audit — 2026-03-16

## Summary
- Total synthesis files: 136
- Refreshable (repo/docs): 59
- Non-refreshable (blog/paper/internal/video): 77
- Missing source_type field: 42 (run --backfill to fix)

## Staleness Breakdown
- Never checked: 59
- Checked < 7 days ago: 0
- Checked 7-30 days ago: 0
- Checked 30+ days ago: 0

## Refreshable Entries by Staleness
| File | Source Type | Source | Last Checked | Days Stale |
|------|------------|--------|-------------|------------|
| cognee-architecture.md | docs | docs.cognee.ai | (never) | 33+ |
| ntfy.md | docs | ntfy.sh | (never) | 5 |
...

## Dead Links
(none detected — run refresh to verify)

---

Error Handling

Scenario	Action
404 / dead link	Mark dead-link, preserve synthesis, report to user
Repo archived	Mark archived, note in Update Log, preserve synthesis
GitHub rate limit	gh api rate_limit, report quota, offer to continue or stop
No changes detected	Mark unchanged, update last_checked, report "up to date"
Context7 no coverage	Fall back to WebFetch
Missing source_type	Auto-detect from URL, warn about --backfill
WebFetch fails	Report error, skip entry, continue with next
Frontmatter parse error	Report file, skip entry, continue with next
No source URL in frontmatter	Skip entry (can't refresh without a source), report

---

Quick Reference

Single File Refresh

1. Read frontmatter → check source_type (auto-detect if missing)
2. Confirm with user
3. Fetch current content (gh api for repos, Context7/WebFetch for docs)
4. Compare with existing raw source in resources/
5. Classify: unchanged / minor / major
6. Report diff summary → wait for confirmation
7. Save new raw source to resources/[topic]-[type]-YYYY-MM-DD.md
8. Verify raw file exists
9. Update synthesis (surgical for minor, re-scaffold for major)
10. Add Update Log entry
11. Update frontmatter (date, last_checked, refresh_status)
12. Update References section
13. Cross-reference check (major changes only)
14. Rebuild INDEX.md

Category/All Refresh

1. Scan files → filter to refreshable → display staleness table
2. Confirm scope with user
3. Process each entry through the single-file workflow above
4. Final summary: N refreshed, N unchanged, N errors

---

Common Mistakes

Mistake	Fix
Overwrote existing raw source file	Always create a NEW file with today's date
Refreshed a blog post or paper	Only repo and docs are refreshable
Skipped user confirmation	Always show diff summary and wait for confirmation
Replaced synthesis instead of updating	Preserve analysis; update facts only
Deleted old raw source	Never delete — raw sources are the version history
Skipped Step 7 (INDEX rebuild)	Always rebuild INDEX.md after any synthesis update
Auto-modified cross-referenced files	Only FLAG related files — never auto-modify
Used WebFetch for GitHub repos	Use gh api for repos — WebFetch is for docs fallback
Refreshed without checking pushed_at	Fast-path skip if no pushes since last_checked
Skipped --backfill warning	If files are missing source_type, suggest --backfill
Changed source URL during refresh	Never change the source URL — it's the canonical reference
Forgot Update Log entry	Every refresh that changes content MUST have an Update Log entry

---

Red Flags — STOP and Fix

• About to overwrite an existing raw source file
• About to refresh a blog, paper, or internal source
• Modifying synthesis without user confirming the diff summary
• No raw source saved before updating synthesis
• Skipped INDEX.md rebuild
• Auto-editing a file that wasn't the target of the refresh
• No Update Log entry after a content change
• refresh_status set to changed but no actual content updates made