Index project dependency paths from wrapper

[st0012]

Summary

Start rubydex_mcp from the Ruby wrapper with the target Bundler context, then pass workspace and dependency roots to the Rust server.

Changes

• Load bundler/setup in the wrapper (Rubydex::MCPServerBridge), inferring BUNDLE_GEMFILE from the target path or cwd.
• Collect Bundler require paths for the active bundle and pass all index roots as argv to the packaged MCP binary.
• Allow the Rust MCP CLI to accept multiple positional paths. canonicalize_path now warns and falls back to the original path instead of panicking on non-UTF-8 paths.
• Document that overlapping index roots are idempotent: the graph keys documents by UriId and overwrites on re-index, so a file discovered through two roots only costs wasted indexing work, never duplicate declarations.
• Broaden the dependency-path collection rescue to StandardError (it touches the filesystem), and document the BUNDLE_GEMFILE side effect plus the workspace-vs-argv contract (only the first argv entry drives the Bundler context; all entries become index roots).
• Document the launcher (MCPServerBridge) in AGENTS.md.

Verification

• bundle exec ruby -Itest test/mcp_server_bridge_test.rb (ENV save/restore, passthrough?, dependency-path collection, empty-argv default)
• cargo test --manifest-path rust/Cargo.toml -p rubydex-mcp (includes an overlapping-roots dedup test asserting a doubly-discovered file yields exactly one definition)
• cargo clippy --manifest-path rust/Cargo.toml -p rubydex-mcp --all-targets -- -D warnings
• cargo fmt --manifest-path rust/Cargo.toml --all --check
• bundle exec rubocop exe/rubydex_mcp lib/rubydex/mcp_server_bridge.rb test/mcp_server_bridge_test.rb
• End-to-end in this repo through bundle exec exe/rubydex_mcp: found workspace declaration Rubydex::MCPServerBridge and dependency declaration Rake::Task.
• End-to-end in a large monolith through the wrapper: indexed over 1.5M declarations and fetched the full MCP-reported descendant set of ActiveRecord::Base through the resolved dependency paths.

[st0012]

• Index project dependency paths from wrapper #821 👈 (View in Graphite)
• Package rubydex MCP executable in gem #819
• main

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