galaxyproject / galaxyproject/loom

Orbit: notebook.md exact-string edits fail and force full-notebook rewrites

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Description

_Context: from a controlled experiment in which eight frontier models (opus, sonnet, gpt, gpt2, gemini-2.5-pro, gemini-3.5-flash, deepseek, haiku) each drove an Orbit session to reanalyze the same RNA-seq dataset (Santana 2023 *C. auris*) on 2026-06-02–04. Evidence quotes are from the per-run `activity.jsonl` logs._

## Problem

Editing `notebook.md` by exact-string match fails when the target text isn't reproduced byte-for-byte, and the brain recovers by rewriting the whole notebook — which churns the `loom-session` / `loom-invocation` tracking blocks.

## Evidence

- **gemini-3.5-flash**: "Could not find the exact text in notebook.md" repeated at 14:52:34 and 14:59:38, after which the agent rewrote the entire notebook, disrupting the tracking blocks.

## Impact

Medium. Full rewrites are slow, risk dropping provenance blocks, and compound the stale-`in_progress` problem (#150).

## Proposed direction

Address notebook edits by section/anchor (the `{#plan-a-step-N}` anchors already exist) rather than exact-string match, or provide an append/replace-section API the brain can target reliably.

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