feat: CLI install command (PR-I1 of 2-PR sequence)

[HumanBean17]

Summary

Implements the install subcommand as PR-I1 of the CLI Install plan (plans/active/PLAN-CLI-INSTALL.md) and propose/active/CLI-INSTALL-PROPOSE.md.

The install command provides an interactive 6-stage setup wizard:

1. Java source detection - Maven/Gradle build file discovery with microservice support
2. Embedding model selection - Path validation with "auto" default
3. Agent host selection - Multi-host support (claude-code, qwen-code, gigacode)
4. Scope selection - Project or user scope
5. Artifact deployment - MCP config merge, skill/agent copy, permission handling
6. Config generation - YAML output + .gitignore update

Key features:

• Non-interactive mode - --non-interactive --agent <host> for CI/automation
• Multi-host support - Configure multiple agents in one run
• Re-run detection - Updates existing config or offers fresh start
• Atomic MCP merge - Preserves existing keys in config files
• Package data - Skill/agent artifacts shipped inside the package

No ontology bump, no re-index required - This is a CLI/UX feature only.

Files Changed

New files

• java_codebase_rag/installer.py - Core installer logic (920 lines)
• java_codebase_rag/install_data/ - Package data for skill + agent artifacts
• tests/test_installer.py - 47 unit tests covering all stages
• tests/test_installer_integration.py - 2 integration tests (gated behind JAVA_CODEBASE_RAG_RUN_HEAVY)

Modified

• pyproject.toml - Added questionary>=2.0 dependency and package_data configuration
• java_codebase_rag/cli.py - Added install subcommand with --non-interactive, --agent, --scope, --model flags

Test Plan

• 47 unit tests pass (all installer stages)
• ruff linting passes
• Existing test suite passes (no regressions)
• install --non-interactive --agent claude-code completes on bank-chat fixture (exit 0)
• install --non-interactive --agent claude-code --agent qwen-code multi-host completes (exit 0)
• Manual interactive testing (TTY prompts)

Integration tests are behind JAVA_CODEBASE_RAG_RUN_HEAVY=1 (same as other e2e tests per tests/README.md).

Usage Examples

# Interactive mode (prompts for all values)
java-codebase-rag install

# Non-interactive, single host
java-codebase-rag install --non-interactive --agent claude-code

# Non-interactive, multiple hosts
java-codebase-rag install --non-interactive --agent claude-code --agent qwen-code

# Custom model
java-codebase-rag install --model /path/to/model.gguf

Dependencies

• Added questionary>=2.0 for interactive prompts
• No other new dependencies (reused existing cli_format.py and cli_progress.py for display)

Next Steps

PR-I2 will implement the update subcommand to refresh shipped artifacts after pip install --upgrade.

Co-Authored-By: Claude Opus 4.7 noreply@anthropic.com

[HumanBean17]

Code Review: PR-I1 — CLI install command

Solid implementation overall. The 6-stage pipeline is well-factored, the prompt() helper cleanly abstracts TTY/non-TTY dispatch, atomic MCP writes are good practice, and test coverage is thorough. Three issues worth fixing before merge:

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Bugs

1. --model silently ignored in non-interactive mode (installer.py:817)

def resolve_model(model_input: str | None, *, non_interactive: bool) -> str:
    if non_interactive or not model_input:  # BUG: short-circuits on non_interactive
        return "auto"

install --non-interactive --model /path/to/model.gguf silently discards the model flag. The condition should check for a provided model before short-circuiting on non_interactive.

2. _deploy_mcp_config ignores merge_mcp_config return value (installer.py:1133)

merge_mcp_config returns False on JSON parse errors, but _deploy_mcp_config always returns success=True. A corrupt .mcp.json or .claude.json is silently treated as a successful deployment. Should propagate the result.

3. Shipped SKILL.md has stale ontology version 16 (install_data/skills/explore-codebase/SKILL.md:457)

The codebase ontology is 17 (ONTOLOGY_VERSION = 17 in ast_java.py:86), but the shipped SKILL.md reads **Ontology: 16**. The original skills/explore-codebase/SKILL.md also says 16 — both need updating to 17.

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Design issues

4. Inconsistent SystemExit handling in run_install (installer.py:1459)

resolve_mcp_command can raise SystemExit(2) but isn't wrapped in try/except like detect_java_directories and select_hosts are. The process still exits with code 2, but the pattern is inconsistent.

5. Partial failure detection uses fragile suffix-based check (installer.py:1474-1478)

if all(r.success for r in results if r.path.suffix in [".json", ".yml", ".yaml"]):

This determines critical vs non-critical failures by file extension. Consider tagging ArtifactResult with an artifact_type field instead.

6. Shipped artifacts are static copies with no sync mechanism

install_data/ files are copies of repo-root originals. No build step or CI check ensures they stay in sync. An ontology bump or tool description change could drift undetected.

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Missing tests vs plan

The plan specifies 54 named tests; implementation has 49 unit + 2 integration. Notable gaps:

Plan #	Test	Why it matters
12	test_yaml_generation_does_not_write_source_root_or_index_dir	Guards against config key regression
34	test_confirm_source_root_interactive_changes_path	Non-default path flow
35	test_confirm_source_root_interactive_invalid_path_reprompts	Re-prompt loop
42, 44-45	test_resolve_mcp_command_not_found_interactive_*	Interactive fallback path
50	test_select_hosts_interactive_all_checked_by_default	Checkbox default behavior

The plan contract says: "If you add, drop, or rename tests, update the plan/prompt text in the same change." The plan file hasn't been updated to reflect the drops.

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Summary

Fix items 1-3 (bugs), update the plan file for the test drops, and this is ready to merge. Items 4-6 are non-blocking improvements that can be addressed in a follow-up or in PR-I2.