After updating swamp from 20260702.214253.0-sha.8411d6d9 to 20260702.230118.0-sha.3ad6e1e2, swamp update synced bundled global skills into several default agent directories and created ~/.agents/skills, even though this repository is configured to use a custom pi agent with skills stored in ~/.pi/agent/skills.

This caused a skill conflict/noise for a repo whose .swamp.yaml enrolls only pi.

Observed output

16:03:44.024   info    update               "20260702.214253.0-sha.8411d6d9" → "20260702.230118.0-sha.3ad6e1e2"
16:03:44.025   info    update               SHA-256 integrity check passed
16:03:44.025   info    update               The swamp binary has been updated globally.
16:03:44.025   info    update               Run `swamp repo upgrade` in your repositories to update settings and instructions.
⠋ Syncing global skills...16:03:44.035   info    update               Synced global skills to "/var/home/evrardjp/.claude/skills"
16:03:44.041   info    update               Synced global skills to "/var/home/evrardjp/.agents/skills"
16:03:44.048   info    update               Synced global skills to "/var/home/evrardjp/.kiro/skills"

Repository configuration

Current repo: /var/home/evrardjp/git/evrardjp/local-infra

.swamp.yaml:

swampVersion: 20260702.230118.0
initializedAt: '2026-06-16T15:47:57.475Z'
repoId: 7ca027d4-3ead-462e-a076-0aa275fe6c30
tools:
  - pi
gitignoreManaged: true
upgradedAt: '2026-07-03T16:04:07.396Z'

.swamp-custom-tools.yaml:

tools:
  - name: pi
    skillsDir: ~/.pi/agent/skills
    instructionsFile: AGENTS.md
    instructionsMode: shared
    skillReferenceStyle: path
    gitignoreEntries: |-
      # Pi skills (managed by swamp)
      ~/.pi/agent/skills/

Actual filesystem state after update

The update created/synced global skills into these directories:

~/.agents/skills/swamp/SKILL.md
~/.agents/skills/swamp-getting-started/SKILL.md
~/.claude/skills/swamp/SKILL.md
~/.claude/skills/swamp-getting-started/SKILL.md
~/.kiro/skills/swamp/SKILL.md
~/.kiro/skills/swamp-getting-started/SKILL.md

~/.pi/agent/skills exists and is the configured custom destination for this repo, but swamp update did not report syncing there.

Why this appears to happen

From the behavior, swamp update seems to run a global skill synchronization step that targets built-in/default agent locations (~/.claude/skills, ~/.agents/skills, ~/.kiro/skills) independently of repository enrollment and independently of .swamp-custom-tools.yaml custom tool definitions. In other words, the update-time global skill sync appears to use a hard-coded/default tool list rather than the configured/enrolled tool list or custom skillsDir.

This is especially surprising because swamp repo upgrade --help documents the enrolled tool list behavior (--tool replaces enrolled tools, omit preserves existing list), and this repo's enrolled list is only pi.

Expected behavior

One of:

swamp update should only sync global skills to configured/enrolled agent skill directories, including custom tools like pi with skillsDir: ~/.pi/agent/skills; or
it should not create/sync any agent skill directory unless the user/repo has explicitly enrolled that agent; or
if update intentionally manages a separate global default agent set, that should be configurable and clearly documented, and it should include a way to opt out of default locations.

At minimum, swamp update should not silently create ~/.agents/skills on a machine/repo configured only for a custom pi agent.

Environment

swamp 20260702.230118.0-sha.3ad6e1e2
binary: /var/home/evrardjp/.local/bin/swamp
repo: /var/home/evrardjp/git/evrardjp/local-infra
enrolled repo tools: pi
custom pi skillsDir: ~/.pi/agent/skills

02Bog Flow

Shipped

7/3/2026, 8:33:46 PM

Click a lifecycle step above to view its details.

03Sludge Pulse

stack72 assigned stack727/3/2026, 4:09:23 PM

evrardjp commented 7/3/2026, 4:08:42 PM

Additional source-level confirmation from the compiled binary/source-map strings:

runs whenever is true.
does:
defines for the built-ins only:

So the root cause is not just inferred behavior: update-time sync explicitly enumerates all built-in keys, deduplicates them, and writes to those global paths. It does not read the repo's enrolled list and cannot include custom tool definitions such as / .

evrardjp commented 7/3/2026, 4:08:55 PM

Correction/clarification to previous ripple: source-level confirmation from the compiled binary/source-map strings:

update.ts runs syncGlobalSkills(ctx.logger) whenever renderer.updated is true.
syncGlobalSkills does:

const allTools = Object.keys(GLOBAL_SKILL_DIRS);
globalDirs = resolveUniqueGlobalSkillsDirs(allTools);
// then copySkillsTo(dir) for each resolved dir

skill_dirs.ts defines GLOBAL_SKILL_DIRS for the built-ins only:

{
  claude: ".claude/skills",
  cursor: ".agents/skills",
  opencode: ".agents/skills",
  codex: ".agents/skills",
  copilot: ".agents/skills",
  kiro: ".kiro/skills"
}

So the root cause is not just inferred behavior: update-time sync explicitly enumerates all built-in GLOBAL_SKILL_DIRS keys, deduplicates them, and writes to those global paths. It does not read the repo's enrolled tools: list and cannot include custom tool definitions such as pi / ~/.pi/agent/skills.

stack72 commented 7/3/2026, 8:33:53 PM

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

First-class scheduled garbage collection policy per datastore namespace

Fine-grained scopes for swamp.club access tokens

Bundled extension model cannot deserialize AWS SDK S3 XML that works in direct Deno

Email invitation is not linked to account created from invite URL

Guide agents to inspect reports after failed model and workflow runs

Add a 'my collective extensions' filter to extensions page

Regression: swamp update syncs global skills to unconfigured agent directories

swamp serve crashes with JavaScript heap OOM while running scheduled workflows

swamp serve startup/shutdown is very slow on large repo and lacks diagnostics

swamp serve should survive bad extension failures

[@adam/cfgmgmt] SSH helper can crash swamp serve via unhandled finally() rejection

Allow swamp clients to send custom headers when connecting to swamp serve

MethodContext docs/comments mention context.putSecret but runtime exposes vaultService.put

install.sh still points users to systeminit/swamp

Support user systemd units for 'swamp serve daemon enable'

Support installing swamp via mise GitHub backend

Allow changing an existing issue to security/confidential after submission

Allow dynamic object expressions for workflow task inputs/globalArgs

Login success still shows login tip

Support confidential visibility for non-security issues

swamp update syncs global skills to default agent directories instead of configured custom Pi skillsDir

Badge for activity on other people's issues

doctor extensions reports source-mounted bundles as unreferenced after repair

Agent setup suggests repo init in already initialized repos

repo upgrade reports success but extension commands still warn about pending migration

model evaluate is slow resolving data.latest expressions in large datastores

Add SSH host public key collection for host certificate workflows

Extension detail page shows deno doc module-not-found failure for published extension

Resolve dynamic workflow task targets inside forEach

Can't click on repository from swamp extension search.

swamp serve does not open the UI

Add deprecate/yank/unyank actions for own extensions on the web interface

swamp update --setup-auto does not work with bluefin44 (crontab not found, should

Terminal rendering breaks at large font sizes

Relationships

#943 swamp update syncs global skills to default agent directories instead of configured custom Pi skillsDir

Summary