feat: reindex:all and daemon:install commands

[jordanpartridge]

Summary

• reindex:all — Incrementally re-indexes and vectorizes all git repos in a configurable base path. Supports --kind, --skip-vectorize, --path flags.
• daemon:install — Generates and installs systemd timer units using the current user/paths at install time. Three timers: enhance (15min), sync (30min), reindex (6h). --status to check, --uninstall to remove.
• No bash scripts, no hardcoded server names. Portable across any systemd host.

Test plan

• 1177 tests pass, coverage 96.1% (threshold 95%)
• PHPStan level 8 clean
• Pint formatted
• know daemon:install on target server
• systemctl list-timers | grep knowledge shows 3 timers

Generated with Claude Code

Summary by CodeRabbit

• New Features

  • Added daemon installation and management command for installing, uninstalling, and monitoring background services.
  • Added batch command to incrementally reindex and vectorize multiple git repositories with configurable options.

• Tests

  • Added comprehensive test coverage for daemon installation command.
  • Added comprehensive test coverage for repository reindexing command.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 4ee71a1e-1816-44cf-b5ae-42a2e89afd70

📥 Commits

Reviewing files that changed from the base of the PR and between 6020a3f and 2cf8c44.

📒 Files selected for processing (4)

• app/Commands/DaemonInstallCommand.php
• app/Commands/ReindexAllCommand.php
• tests/Feature/Commands/DaemonInstallCommandTest.php
• tests/Feature/Commands/ReindexAllCommandTest.php

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📝 Walkthrough

Walkthrough

This PR introduces two new Laravel Zero commands: DaemonInstallCommand manages systemd timers and services for knowledge daemons (enhance, sync, reindex), while ReindexAllCommand orchestrates incremental reindexing and vectorization across multiple git repositories. Both commands include comprehensive tests.

Changes

Cohort / File(s)	Summary
Daemon Management app/Commands/DaemonInstallCommand.php, tests/Feature/Commands/DaemonInstallCommandTest.php	New command for installing/uninstalling/managing systemd timers and services. Builds service and timer unit definitions, manages lifecycle via systemctl, and reports status. Tests cover non-systemd scenarios, timer presence detection, and status output.
Repository Reindexing app/Commands/ReindexAllCommand.php, tests/Feature/Commands/ReindexAllCommandTest.php	New command that iterates git repositories and orchestrates incremental symbol reindexing via SymbolIndexService and optional vectorization via CodeIndexerService. Validates paths, enumerates repos, reports per-repo and aggregate results. Tests cover invalid paths, empty/missing repos, indexing failures, and skip-vectorize flag behavior.

Sequence Diagrams

sequenceDiagram
    participant User
    participant DaemonCommand as DaemonInstallCommand
    participant Process as Process Facade
    participant SystemD as systemd
    participant FileSystem as /etc/systemd/system

    User->>DaemonCommand: handle() with --install
    DaemonCommand->>DaemonCommand: determine user, home, PHP binary
    loop for each unit (enhance, sync, reindex)
        DaemonCommand->>DaemonCommand: buildService() & buildTimer()
        DaemonCommand->>FileSystem: write temp files
        DaemonCommand->>Process: copy to /etc/systemd/system
        DaemonCommand->>Process: systemctl daemon-reload
        DaemonCommand->>Process: systemctl enable timer
        DaemonCommand->>Process: systemctl start timer
    end
    DaemonCommand->>DaemonCommand: showStatus()
    DaemonCommand->>User: display timer status

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sequenceDiagram
    participant User
    participant ReindexCommand as ReindexAllCommand
    participant FileSystem as File System
    participant SymbolService as SymbolIndexService
    participant CodeService as CodeIndexerService

    User->>ReindexCommand: handle() with --path --skip-vectorize
    ReindexCommand->>FileSystem: validate base path
    ReindexCommand->>FileSystem: enumerate git repositories
    loop for each git repository
        ReindexCommand->>SymbolService: indexFolder() with symbol kinds
        SymbolService-->>ReindexCommand: success + symbol_count
        alt skip-vectorize not set
            ReindexCommand->>CodeService: ensureCollection()
            ReindexCommand->>CodeService: vectorizeFromIndex()
        end
        ReindexCommand->>User: report per-repo results
    end
    ReindexCommand->>User: display aggregate results

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~22 minutes

Possibly related PRs

• feat: code vectorization pipeline and search-code MCP tool #136: Introduces indexSymbol(), vectorizeFromIndex(), and ensureCollection() methods in CodeIndexerService that directly support the reindexing and vectorization flows in ReindexAllCommand.

Poem

🐰 A daemon hops through systemd land,
Timers tick and services expand,
Knowledge blooms across each repo bright,
Reindexing magic, vectorizing light!
Burrow deep, the wisdom grows—
Where knowledge daemons go! 🌱

✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feature/code-vectorization-mcp

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[github-actions]

📊 Coverage Report

Metric	Coverage	Threshold	Status
Lines	96.1%	95%	✅

Files Below Threshold

File	Coverage	Uncovered Lines
app/Enums/ObservationType.php	0%	None
app/Exceptions/Qdrant/QdrantException.php	0%	None
app/Integrations/Qdrant/Requests/ScrollPoints.php	0%	None
app/Mcp/Servers/KnowledgeServer.php	0%	None
app/Services/AgentHealthService.php	0%	None
app/Commands/DaemonInstallCommand.php	23.1%	57, 58, 61, 66, 67... (+55 more)
app/Mcp/Tools/RememberTool.php	66.7%	106, 107, 108, 109, 110... (+19 more)
app/Commands/ReindexAllCommand.php	67.3%	31, 32, 91, 92, 94... (+13 more)
app/Mcp/Tools/CorrectTool.php	70.4%	53, 54, 55, 56, 57... (+3 more)
app/Mcp/Tools/SearchCodeTool.php	72.7%	72, 73, 74, 75, 76... (+7 more)

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🏆 Synapse Sentinel Gate

[github-actions]

🏆 Sentinel Certified

✅ Tests & Coverage: 0 tests passed
✅ Security Audit: No security vulnerabilities found
✅ Pest Syntax: All test files use describe/it syntax

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