Sync pinned Pi packages

[yourconscience]

What changed

• new Pi-only packages list on agent targets: sync reconciles ~/.pi/agent/settings.json package declarations; Pi installs missing declared packages at startup
• *[]string pointer keeps absent (no management) distinct from [] (clear packages)
• package removals and filtered-entry replacement join the setup confirmation gate; declining suppresses the rewrite
• null/malformed settings.json return errors instead of panicking
• package managed/drifted/remove counts in status, sync, and verbose reports

Verification

• go test ./..., git diff --check
• gate review by independent read-only reviewer: no blocking findings
• end-to-end: Pi 0.85.1 + 6 pinned packages installed on a second machine, RPC smoke loads mcp/subagents/feynman/todo commands

Summary by Sourcery

Support declarative synchronization of pinned Pi packages while preserving existing settings and protecting destructive changes with confirmation.

New Features:

• Add optional pinned package declarations for Pi targets and reconcile them with Pi's agent settings.
• Report managed, drifted, and removed Pi packages across status, sync, and verbose output.

Bug Fixes:

• Handle null or malformed Pi settings files with errors instead of panics.

Enhancements:

• Preserve unrelated Pi settings while replacing non-canonical package entries.
• Require confirmation for destructive package changes and honor declined synchronization.

Documentation:

• Document Pi package declarations, startup installation behavior, and troubleshooting guidance.

Tests:

• Add coverage for package synchronization, settings preservation, filtered-entry replacement, empty declarations, invalid settings, target validation, and confirmation handling.

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[sourcery-ai]

Reviewer's Guide

Adds opt-in, Pi-only pinned package management by validating an optional package list, reconciling it into Pi’s settings.json without disturbing unrelated settings, gating destructive changes during sync, and surfacing package state in reports and documentation.

Sequence diagram for Pi package synchronization

sequenceDiagram
    participant User
    participant Sync as dotagents_sync
    participant Inspect as inspectAgent
    participant Settings as Pi_settings_json
    participant Pi

    User->>Sync: runSync()
    Sync->>Inspect: augmentPiPackageReport()
    Inspect->>Settings: readPiPackages()
    Settings-->>Inspect: declared packages and exactness
    Inspect-->>Sync: package drift and removal actions
    alt destructive package changes
        Sync->>User: confirmDestructiveSyncActions()
        alt user accepts
            Sync->>Settings: syncPiPackages()
            Settings-->>Sync: rewritten packages list
        else user declines
            Sync-->>User: preserve existing declarations
        end
    else package list already synchronized
        Sync-->>User: report managed packages
    end
    Pi->>Settings: read packages at startup
    Pi-->>Pi: install missing declared packages

Loading

File-Level Changes

Change	Details	Files
Add Pi-only package declarations with absent-versus-empty semantics and validation.	Add an optional pointer-backed YAML packages field to agent targets. Trim and reject empty or duplicate package names. Reject package configuration on non-Pi targets.	cmd/dotagents/main.go cmd/dotagents/config.go cmd/dotagents/pi_packages_test.go README.md
Reconcile declared Pi packages with ~/.pi/agent/settings.json while preserving unrelated settings.	Read and validate JSON settings, including explicit errors for null or malformed content. Detect exact package-list matches, drift, removals, and replacement of non-string entries. Write the canonical package list while retaining other settings and creating parent directories as needed.	cmd/dotagents/pi_packages.go cmd/dotagents/pi_packages_test.go
Integrate Pi package reconciliation into inspection and sync workflows with destructive-action confirmation.	Apply package updates during sync only for detected Pi targets with package management enabled. Route package removals and filtered-entry replacement through the setup confirmation gate. Skip package rewrites when the user declines destructive changes.	cmd/dotagents/inspect.go cmd/dotagents/sync.go cmd/dotagents/setup_scaffold.go cmd/dotagents/setup_separation_test.go
Expose package management state and actions across reporting surfaces.	Track managed, drifted, update, and removal package entries in agent reports. Include package state in synced determination, sorting, status/drift buckets, verbose output, and sync action counts.	cmd/dotagents/main.go cmd/dotagents/inspect.go cmd/dotagents/report.go
Document Pi package pinning, installation behavior, and troubleshooting.	Document the packages YAML configuration and settings.json reconciliation. Clarify that Pi must be installed separately and installs declared packages at startup. Add guidance for missing Pi packages.	README.md docs/troubleshooting.md skills/dotagents/SKILL.md

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