Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add flonat/flonat-research --skill pipeline-manifestgit clone --depth 1 https://github.com/flonat/flonat-researchWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/flonat/flonat-research/pipeline-manifest)<a href="https://agentmods.dev/skills/flonat/flonat-research/pipeline-manifest"><img src="https://agentmods.dev/badge/skills/flonat/flonat-research/pipeline-manifest/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/flonat/flonat-research/pipeline-manifest"><img src="https://agentmods.dev/badge/skills/flonat/flonat-research/pipeline-manifest.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00055 | $0.02494 |
| Opus 5.5 | $0.00022 | $0.00998 |
| Sonnet 5.5 | $0.00011 | $0.00499 |
| Haiku 4.5 | $0.00006 | $0.00249 |
Grade A, and why
pipeline-manifest scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 227 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Pipeline Manifest
Build and maintain a pipeline.md that maps every script in a research project to its inputs, outputs, and the paper figures/tables it feeds. Optionally add structured headers to scripts that lack them.
When to Use
- When starting a multi-step empirical project (establish the pipeline early)
- Before sharing code with coauthors (makes the data flow legible)
- Before submission (ensures the replication package is traceable)
- After inheriting or reviving old code (pair with
code-archaeology) - When you can't remember which script produces Figure 3
When NOT to Use
- Pure theory projects with no empirical pipeline
- Single-script projects (no pipeline to map)
- Code quality review — use the
code-reviewagent instead (this skill maps structure, not quality)
Modes
Ask the user which mode to run:
| Mode | What it does | Writes to |
|---|---|---|
| Scan (default) | Read-only. Scans scripts, builds pipeline.md |
pipeline.md only |
| Add headers | Scan + insert structured headers into scripts that lack them | pipeline.md + script files |
In Add headers mode, show the proposed header for each script and get confirmation before writing. Never overwrite an existing structured header — only add to scripts that lack one.
Structured Script Header Format
Every research script should begin with a structured header block. The format adapts to the language:
Python
# ============================================================================
# PURPOSE: [One sentence describing what this script does]
# INPUTS: [Comma-separated list of input files, relative to project root]
# OUTPUTS: [Comma-separated list of output files, relative to project root]
# DEPENDS: [Scripts that must run before this one, or "none"]
# PAPER: [Figure/table references this feeds, e.g. "Figure 2, Table 1", or "none"]
# ============================================================================
R
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 227 lines · 55 tokens per session scan A efc81f87d410
pipeline-manifest is a skill published in the GitHub repository flonat/flonat-research (147 stars, last pushed 28d ago), licensed MIT. It adds 55 tokens to every session and 2,494 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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