paths.base: manifest is not honored for workflows: — bundled workflows only resolve from repo root, blocking self-contained subdir layouts (sibling to #459)

A directory that contains a .swamp/ runtime directory but no .swamp.yaml marker is a partially-initialized or corrupted repository. swamp does not detect this distinct state — every repo-requiring command emits the same generic error it would for a directory with no .swamp/ at all:

Error: "Not a swamp repository: <dir>. To initialize a new repository, run 'swamp repo init', or specify an existing repository with 'swamp <command> --repo-dir /path/to/repo'."

There is no hint that a .swamp/ directory is already present (i.e. that this is likely a broken/partial repo rather than a fresh directory), and swamp doctor doesn't flag it.

Steps to reproduce

mkdir orphan && cd orphan && mkdir .swamp — simulates an orphaned/partial .swamp/ (e.g. from an interrupted swamp repo init, a deleted .swamp.yaml, or a stray .swamp/ created by another command).
Run any repo-requiring command, e.g. swamp model search or swamp extension quality <manifest>.

Actual

Generic Not a swamp repository: <dir> — identical to the no-.swamp/-at-all case. (The suggested swamp repo init does recover it, silently reusing the existing .swamp/ directory.)

Expected

Detect a .swamp/ present without a valid .swamp.yaml and report it distinctly, e.g.:

Found a .swamp/ directory but no .swamp.yaml marker — the repository looks partially initialized or corrupted. Run swamp repo init --force to repair.

A swamp doctor check for an orphaned/partial .swamp/ (and ideally a warning before a plain swamp repo init silently reuses a stale .swamp/ DB) would also help.

How I hit it

On a real workspace the repository root had a .swamp/ directory but no .swamp.yaml, so swamp extension quality <subdir>/manifest.yaml run from the root failed with the generic message even though .swamp/ was clearly present. It took a while to realize the marker was missing rather than the directory not being a repo. It would also be worth investigating how a .swamp/ can come to exist at a location where swamp repo init never completed, to prevent the orphaned state from arising in the first place.

Environment

swamp 20260526.194925.0-sha.80b42672
macOS (darwin)

02Bog Flow

Shipped

5/27/2026, 10:44:18 PM

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03Sludge Pulse

stack72 assigned stack725/27/2026, 8:07:57 PM

stack72 commented 5/27/2026, 11:01:56 PM

Thanks @magistr for reporting this! The fix has been merged and a release is on its way. We appreciate your contribution to swamp.

Should be able to see all the issues I created by a filter "submitted by me"

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feat: giga-swamp phase 4 — CEL cross-namespace queries

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swamp issue: add ability to edit issue title and body after submission

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Allow global arguments in direct type execution (workflow fan-out)

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Enforce adversarial review gate before extension push

support git forge / web namespaces for collectives

Report type filtering in report search

extension search: empty results from CLI despite known extensions

workflow approve/resume cannot find suspended runs

vault annotate --url fails with query params on @swamp/aws-sm

datastore compact VACUUM fails with ERR_SQLITE_ERROR

workflow approve/resume cannot find suspended run when using S3 datastore

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AWS: support vault expressions for credentials instead of env-var/SDK-chain-only auth

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Support vault expressions for API token instead of env var

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