Lab #1051: Regression: swamp update syncs global skills to unconfigured agent directories

Summary

After updating swamp from 20260708.012813.0-sha.0f7166fe to 20260709.014917.0-sha.3da10c76, swamp update synced global skills into multiple agent directories even though the config only declares the Pi tool skills directory.

Actual behavior

swamp update copied/synced global skills to:

/var/home/[REDACTED]/.claude/skills
/var/home/[REDACTED]/.agents/skills
/var/home/[REDACTED]/.kiro/skills
/var/home/[REDACTED]/.pi/agent/skills

Update log:

[IP-1].774   info    update               "20260708.012813.0-sha.0f7166fe" →
                                            "20260709.014917.0-sha.3da10c76"
[IP-1].777   info    update               SHA-256 integrity check passed
[IP-1].777   info    update               The swamp binary has been updated globally.
[IP-1].777   info    update               Run `swamp repo upgrade` in your repositories to update settings
                                            and instructions.
[IP-1].794   info    update               Synced global skills to "/var/home/[REDACTED]/.claude/skills"
[IP-1].801   info    update               Synced global skills to "/var/home/[REDACTED]/.agents/skills"
⠦ Syncing global skills...[IP-1].808   info    update               Synced global skills to "/var/home/[REDACTED]/.kiro/skills"
[IP-1].815   info    update               Synced global skills to "/var/home/[REDACTED]/.pi/agent/skills"

Expected behavior

swamp update should only sync skills to the configured tool skills directory/directories. In this setup, that means only ~/.pi/agent/skills. It should not create or update skills under Claude, .agents, or Kiro directories when those tools are not configured.

Config

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

Regression window

Observed immediately after updating from 20260708.012813.0-sha.0f7166fe to 20260709.014917.0-sha.3da10c76. This appears to be a regression of prior behavior around not copying skills into unconfigured agent directories.

Impact

Unexpected writes to user home directories for tools that are not configured, causing skill duplication and pollution of unrelated agent/tool setups.

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Relationships

#1051 Regression: swamp update syncs global skills to unconfigured agent directories