feat(setup): add CommandCode CLI as supported agent

[eSagraAI]

🔗 Linked Issue

Closes #1119

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🏷️ PR Type

• type:bug — Bug fix
• type:feature — New feature
• type:docs — Documentation only
• type:refactor — Code refactoring (no behavior change)
• type:chore — Maintenance, dependencies, tooling
• type:breaking-change — Breaking change

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📝 Summary

• Adds commandcode as a declarative agent in agentAdapters() — no custom installer, the generic injectMCP / writeInstruction driver handles both writes.
• engram setup commandcode registers mcpServers.engram in the user-scope ~/.commandcode/mcp.json (private, available across all projects).
• Writes the Memory Protocol as a marker block into the user-tier ~/.commandcode/AGENTS.md, preserving user preferences and staying idempotent (CommandCode re-reads memory every request, so no restart needed for AGENTS.md).

📂 Changes

File	Change
internal/setup/registry.go	New commandCodeObject MCP format ({transport:"stdio", enabled:true, command, args} under mcpServers) + mcpEntry case
internal/setup/agents.go	New commandcode registry entry plus commandcodeDir / commandcodeMCPPath / commandcodeAgentsPath helpers
internal/setup/registry_test.go	commandcode row in declarativeAgents(), in expected SupportedAgents(), and transport/enabled shape assertions
cmd/engram/main.go	commandcode added to the setup [agent] usage line
cmd/engram/main_test.go	commandcode in usage list and a printPostInstall case
README.md	CommandCode row in supported-agents table
docs/AGENT-SETUP.md	CommandCode table row, ## CommandCode section, format note in intro

🧪 Test Plan

• Unit tests pass locally: go test ./...
• E2E tests pass locally: go test -tags e2e ./internal/server/...
• Lint passes locally: make lint
• Manually tested the affected functionality

go test ./... is NOT green: the only 2 failures (TestInstallPiInstallsPackagesAndWritesConfig in internal/setup, TestDetectProjectFull_ChildScanFindsLaterSecondRepository in internal/project) reproduce identically on a clean tree without this change (verified via git stash -u), so they are pre-existing environment failures, not regressions. Deliberately left unchecked rather than marked PASS.

Manual verification — engram setup commandcode against an isolated HOME:

✓ Installed commandcode plugin (2 files)

.commandcode
├── AGENTS.md
└── mcp.json

{
  "mcpServers": {
    "engram": {
      "command": "<absolute-path-to>/engram",
      "enabled": true,
      "transport": "stdio",
      "args": ["mcp", "--tools=agent"]
    }
  }
}

Re-running is idempotent (1 marker block). The real CLI accepts the generated file: cmd mcp list shows engram / stdio / user / enabled and cmd mcp get engram reports the correct transport, command and args.

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🤖 Automated Checks

These run automatically and all must pass before merge:

Check	What it verifies	Status
Check Issue Reference	PR body contains Closes #N / Fixes #N / Resolves #N	⏳
Check Issue Has status:approved	Linked issue has status:approved label	⏳
Check PR Has type:* Label	PR has exactly one type:* label	⏳
Unit Tests	go test ./... passes	⏳
E2E Tests	go test -tags e2e ./internal/server/... passes	⏳
Plugin Tests	npm test passes in plugin/pi	⏳
Lint	golangci-lint reports no new findings	⏳

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✅ Contributor Checklist

• I linked an approved issue above (Closes #1119)
• I added exactly one type:* label to this PR
• I ran unit tests locally: go test ./...
• I ran e2e tests locally: go test -tags e2e ./internal/server/...
• I ran lint locally: make lint
• Docs updated (if behavior changed)
• Commits follow conventional commits format
• No Co-Authored-By trailers in commits

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💬 Notes for Reviewers

1. New mcpFormat instead of reusing mcpServersObject. The issue left the stdio shape as an open verification point; it was verified empirically with the real CLI (cmd mcp add --scope user engram-probe -- … → cmd mcp get, probe removed and the user config restored byte-identical afterwards): CommandCode writes {transport:"stdio", enabled:true, command, args}. A bare {command, args} entry would omit the transport discriminator, so a new format value was added following the serversObject / opencodeObject precedent.
2. markerBlock, not wholeFile. Unlike Cline (dedicated rules dir), ~/.commandcode/AGENTS.md is a shared user-preferences file read cumulatively with project/subdirectory tiers — same reasoning as the qwen/kilocode adapters.
3. No plugin, no hooks — thin adapter per skills/plugin-thin, exactly as scoped in feat(setup): add CommandCode CLI as supported agent #1119. docs/INSTALLATION.md untouched, mirroring PR feat(setup): add Cline CLI as supported agent #1116 (6-file scope + the new-format hunk).

Summary by CodeRabbit

• New Features

  • Added CommandCode as a supported agent for setup.
  • CommandCode setup now configures the Engram MCP server and Memory Protocol instructions.
  • Added verification guidance, including required session restart steps and Windows CLI details.

• Documentation

  • Added CommandCode to the agent setup quick reference and expanded configuration documentation.

• Tests

  • Added coverage for CommandCode support, configuration, usage output, and post-install instructions.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: ASSERTIVE

Plan: Advanced

Run ID: 28b17d10-da9c-4d4a-aa03-f45e76bbdb4f

📥 Commits

Reviewing files that changed from the base of the PR and between 5d5bf83 and b075cac.

📒 Files selected for processing (7)

• README.md
• cmd/engram/main.go
• cmd/engram/main_test.go
• docs/AGENT-SETUP.md
• internal/setup/agents.go
• internal/setup/registry.go
• internal/setup/registry_test.go

Included review availability: Your plan provides up to 8 included reviews per hour; 7 remain after this review.

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📝 Walkthrough

Walkthrough

The setup registry now supports CommandCode through ~/.commandcode/mcp.json and ~/.commandcode/AGENTS.md. CLI help, post-install output, tests, README content, and setup documentation include the new agent.

Changes

CommandCode setup support

Layer / File(s)	Summary
CommandCode registration and paths internal/setup/registry.go, internal/setup/agents.go	Adds the CommandCode MCP format, stdio metadata, enabled status, command path, MCP arguments, and user-scope file paths.
CommandCode registry validation internal/setup/registry_test.go	Registers commandcode as a declarative agent and verifies its MCP entry metadata.
CommandCode CLI and documentation cmd/engram/main.go, cmd/engram/main_test.go, README.md, docs/AGENT-SETUP.md	Adds CommandCode to setup help, post-install checks, supported-agent lists, and setup documentation.

Estimated code review effort: 2 (Simple) | ~10 minutes

Severity of issue fixed: Medium

Suggested reviewers: alan-thegentleman

Sequence Diagram(s)

sequenceDiagram
  participant User
  participant EngramSetup
  participant CommandCodeMCP
  participant CommandCodeMemory
  User->>EngramSetup: Run engram setup commandcode
  EngramSetup->>CommandCodeMCP: Write mcpServers.engram
  EngramSetup->>CommandCodeMemory: Write Memory Protocol marker block
  EngramSetup-->>User: Display verification and restart guidance

Loading

Merge Risk: ⚪ Minimal · up to b075c

No actionable merge-blocking risk remains in the CommandCode setup integration.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 12 functions across 5 files. (2 skipped: …	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely identifies the primary change: adding the CommandCode CLI as a supported setup agent.
Linked Issues check	✅ Passed	The changes satisfy issue #1119. They add the declarative CommandCode registry entry, use the user-scoped ~/.commandcode/mcp.json path with the CommandCode MCP format, inject the Memory Protocol into …
Out of Scope Changes check	✅ Passed	The changes are limited to the CommandCode adapter, registry format, setup help, documentation, and related tests. No unrelated code or feature changes are present.

Full details: Docstring Coverage

Explanation

Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 12 functions across 5 files. (2 skipped: 2 unsupported.)

• Fix all pre-merge checks with AI

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests

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