Defer sort seed checks until adjust-order startup

.claude/skills/trellis-spec-bootstarp/references/mcp-setup.md

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+# MCP Setup
+
+GitNexus and ABCoder are recommended when bootstrapping Trellis specs because they expose architecture and AST context to the agent. They are tool choices, not platform requirements. Configure them through whatever MCP mechanism your agent host provides.
+
+## GitNexus
+
+GitNexus builds a code knowledge graph from the repository. Use it for module boundaries, execution flows, dependency relationships, blast radius, and graph queries.
+
+### Install and Index
+
+```bash
+# Run from the repository root.
+npx gitnexus analyze
+
+# Check index status.
+npx gitnexus status
+
+# Re-index after code changes when the analysis is stale.
+npx gitnexus analyze
+```
+
+The index is written to `.gitnexus/`. Keep embeddings only if the project already uses them; otherwise a normal index is enough for spec bootstrapping.
+
+### MCP Server Command
+
+Use this server command in the host's MCP configuration:
+
+```bash
+npx -y gitnexus mcp
+```
+
+### Useful Tools
+
+| Tool | Purpose |
+|------|---------|
+| `gitnexus_query` | Find execution flows and functional areas by concept |
+| `gitnexus_context` | Inspect callers, callees, references, and process participation for a symbol |
+| `gitnexus_impact` | Understand blast radius before changing a symbol |
+| `gitnexus_detect_changes` | Check changed symbols and affected flows before finishing |
+| `gitnexus_cypher` | Run direct graph queries |
+| `gitnexus_list_repos` | List indexed repositories |
+
+## ABCoder
+
+ABCoder parses code into UniAST and gives precise package, file, and node-level structure. Use it for signatures, type shapes, implementations, dependencies, and reverse references.
+
+### Install
+
+```bash
+go install github.com/cloudwego/abcoder@latest
+abcoder --help
+```
+
+### Parse Repositories
+
+```bash
+abcoder parse /absolute/path/to/package \
+  --lang typescript \
+  --name package-name \
+  --output ~/abcoder-asts
+```
+
+For monorepos, parse each package with a stable `--name` so task notes can reference the same repository names.
+
+### MCP Server Command
+
+Use this server command in the host's MCP configuration:
+
+```bash
+abcoder mcp ~/abcoder-asts
+```
+
+### Useful Tools
+
+| Tool | Layer | Purpose |
+|------|-------|---------|
+| `list_repos` | 1 | List parsed repositories |
+| `get_repo_structure` | 2 | Inspect packages and files |
+| `get_package_structure` | 3 | Inspect nodes within a package |
+| `get_file_structure` | 3 | Inspect functions, classes, types, and signatures in a file |
+| `get_ast_node` | 4 | Retrieve code, dependencies, references, and implementations |
+
+## Verification
+
+After configuration, verify from the agent host that both MCP servers are visible. Then run one simple query against each server before starting the spec writing pass.
+
+```bash
+ls .gitnexus/meta.json
+ls ~/abcoder-asts/*.json
+```