whole_body_migration — AgentTeamsModule

Retires a legacy whole-body content fence once its template has been split into named sections, and reports a section that appears twice in a merged file. fences calls it from _merge_fenced_content and _detect_duplicate_sections.

Source: agentteams/whole_body_migration.py — integrity-pinned.

Why it exists

A template with no fences is wrapped in one content fence at emit time. When the template gains named sections, the render stops being wrapped. Until 2026-10-11 the merge retired the stale content block only when it was the file's only fence. Files that also carried memory_index_consultation got the named sections added beside it, so every section appeared twice, both copies inside fences (quality-auditor, tool-doc-researcher and conflict-resolution across 12 repositories, in .github/agents and Goose recipes).

The migration

applies(existing, new) is true when content is on disk, absent from a render that has named sections, and the only on-disk fence the render no longer has. A file with a second orphaned fence is not migrated; the duplicate report names its problem instead.

migrate(...) rewrites only the content block, then fences runs the ordinary merge on the result. The other fences update in place, the front matter goes through the three-way merge, and the twin pass runs. The block is replaced by the render's body (its first line to its last fence) with the fences the file already carries cut out. Text outside the block is untouched.

Each heading section of the old body is matched to the render:

Old section	Outcome
Every line survives in the result	dropped
Heading the render keeps unfenced	the deployed copy is kept unless it is provably template text
A user region, or a heading the render does not have	carried out of the fence, unfenced
Equals a past template rendering of its heading (lineage corpus)	dropped
An unproven copy of a section the render fences	not kept when the run has a backup dir (keeping it recreates the duplicate); without one, carried out as a twin that fence_twins keeps and flags
Holds a managed marker, a TOML string delimiter or a Rule S-5 instruction-override pattern	never re-emitted outside the fence (a marker would be forged; injected text would become project-owned)

On a run without a backup dir, text that would survive only in the sidecar makes migrate return None, so the old fence stays and the duplicate report names it; marker and injection text is the exception and is overwritten, as before.

migration_notice names every kept, carried, dropped-as-retired and not-kept section. The notice is a fence 'content': shrink notice, so the old body goes to the .lost.content.md.agentteams-bak sidecar (also under --shrink-policy allow) and fleet reports REVIEW.

The duplicate report

duplicate_notices(merged, added_sids) reports each ##–###### heading that appears more than once, saying where the copies sit. Each notice starts with DUPLICATE_PREFIX (duplicate section), which fleet files as its own REVIEW class (duplicates), not as a shrink notice.

Copies	Reported
One inside a fence, one outside	on every merge
All inside fences, spread over two or more fences	on every merge
All outside fences	only when the merge added a fence
Repeated inside one fence	never (the template's own structure)

Name	Purpose
WHOLE_BODY_FENCE	"content".
DUPLICATE_PREFIX	"duplicate section".
Migration	The rewritten file and what happened to each old section.
applies(existing_regions, new_regions)	The predicate above.
migrate(new_rendered, existing, existing_regions, *, bridge_blocks=None, twin_source=None, allow_drop=False)	Returns a Migration, or None when the layout cannot be mapped (the render's indentation differs, or it has no fence).
migration_notice(mig, *, has_tail)	The notice line.
duplicate_notices(merged, added_sids)	The duplicate report.