What is debug-highlights?

A debugging workflow for checking whether highlights copied from Kobo, an e-reader, to Calibre, an ebook library manager, are converted correctly. It compares the converter’s results with manually created reference highlights.

Use it to investigate incorrect Kobo-to-Calibre highlight positions. It works with the Kobo and Calibre databases, creates comparison data, records logs, and may delete the selected book’s existing highlights.

It helps find errors caused by the two programs storing positions differently, including differences between EPUB and Kobo’s modified book format.

How degiz/kobo2calibre configures Claude Code and Codex

Reuse

Borrowing it

Nothing to install: this file belongs to degiz/kobo2calibre. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/degiz/kobo2calibre/main/.agents/skills/debug-highlights/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/degiz/kobo2calibre

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/degiz/kobo2calibre/debug-highlights/github.svg)](https://agentmods.dev/skills/degiz/kobo2calibre/debug-highlights)

Your own site

<a href="https://agentmods.dev/skills/degiz/kobo2calibre/debug-highlights"><img src="https://agentmods.dev/badge/skills/degiz/kobo2calibre/debug-highlights/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/degiz/kobo2calibre/debug-highlights"><img src="https://agentmods.dev/badge/skills/degiz/kobo2calibre/debug-highlights.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 17 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,326 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00017	$0.01326
Opus 5.5	$0.00007	$0.00530
Sonnet 5.5	$0.00003	$0.00265
Haiku 4.5	$0.00002	$0.00133

Measured 2mo ago against content hash 1eda02c407b8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

debug-highlights 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 2mo 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.

.agents/skills/debug-highlights/SKILL.md · 98 lines

How it starts

The opening of the file, as written. The whole thing — 98 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Debug Highlights Skill

Debug CFI conversion issues by creating manual ground-truth highlights in both systems and comparing converter output.

Config

Read paths.kobo_db and paths.calibre_db from .agents/config.yaml. If the file is missing, ask the user for paths and create it.

Defaults: Kobo KoboReader.sqlite on mounted volume, Calibre metadata.db in library dir
Logs: .agents/logs/debug-highlights-<timestamp>.log
Kepub: Always new format, max verbosity (-vv)

Workflow

WARNING: Deletes all highlights for selected book (preserved in memory, but lost if skill crashes). User should have backups.

IMPORTANT Kobo and Calibre use different versions of the same book: Calibre has a original epub, while Kobo has a kepubified version. The source code of "kepubify" is available in "kepubify.py". If needed, lookup other source code of Calibre.

IMPORTANT Calibre's CFI encode/decode logic lives in cfi.pyj: https://raw.githubusercontent.com/kovidgoyal/calibre/master/src/pyj/read_book/cfi.pyj — key functions: encode(), adjust_node_for_text_offset(), decode(), node_for_text_offset().

IMPORTANT Calibre's kepubify logic (adds kobo spans to EPUB HTML): https://raw.githubusercontent.com/kovidgoyal/calibre/master/src/calibre/ebooks/oeb/polish/kepubify.py — local copy in kepubify.py. Key function: kepubify_html_data().

IMPORTANT Always run calibre-customize -b $(pwd) before calibre-debug -e. The dual import loads the installed plugin, not local files. Symptom of staleness: debug logging you added doesn't appear.

Phase 1: Identify Book

Verify Kobo mounted: test -f /Volumes/KOBOeReader/.kobo/KoboReader.sqlite
Ask user for book name
Query: SELECT DISTINCT VolumeID, COUNT(*) FROM Bookmark WHERE VolumeID LIKE '%?%' AND text != '' GROUP BY VolumeID
User confirms which VolumeID

Phase 2.5: Ground Truth Setup

User selects 1 highlight to test
Preserve all highlights to memory (both DBs)
Delete all existing highlights, including those marked as "removed": DELETE FROM Bookmark WHERE VolumeID = ? and DELETE FROM annotations WHERE book = ?
User creates same highlight manually on Kobo device (unmount, highlight, remount)
Verify: SELECT * FROM Bookmark WHERE VolumeID = ? ORDER BY DateCreated DESC LIMIT 1
User creates same highlight manually in Calibre viewer (must close viewer to save)
Verify: SELECT annot_data FROM annotations WHERE book = ? LIMIT 1
Display both ground truth highlights side-by-side
User confirms ready for conversion

Read the full file on GitHub · 98 lines

Changes

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.

2mo ago First seen · 98 lines · 17 tokens per session scan A 1eda02c407b8

Subscribe to this mod's changes

debug-highlights is a skill published in the GitHub repository degiz/kobo2calibre (23 stars, last pushed 7mo ago), licensed MIT. It adds 17 tokens to every session and 1,326 once invoked, about $0.0001 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 2026-08-30.

Debugging

debug-highlights next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
debug-highlightsdegiz/kobo2calibre	Skill	23	7mo ago	MIT	A	17	Claude Code, Codex
systematic-debuggingopen-metadata/OpenMetadata	Skill	16k	today	Apache-2.0	A	37	Claude Code
log-error-digestzebbern/claude-code-guide	Skill	4.7k	yesterday	MIT	A	71	Claude Code, Codex
cwv-optimizeradobe/skills	Skill	321	today	Apache-2.0	A	112	Claude Code
ci-fixersipyourdrink-ltd/bernstein	Skill	1.2k	today	Apache-2.0	A	15	Claude Code, Codex
incident-response-incident-responsermyndharis/antigravity-skills	Skill	2.0k	yesterday	MIT	A	36	Claude Code, Codex
diagnosing-missing-recordingsPostHog/posthog	Skill	41k	today	none	A	76	Claude Code, Codex

kobo2calibre: Skill for Claude Code