# Verify all tools
npx gitnexus status          # GitNexus indexed?
abcoder list-repos            # ABCoder has ASTs?
codex mcp list                # Codex has MCP servers?
python3 .trellis/scripts/get_context.py  # Trellis initialized?

npx gitnexus analyze

gitnexus_query({query: "plugin system"})        # Find execution flows
gitnexus_context({name: "SomeClass"})            # 360-degree symbol view
gitnexus_cypher({query: "MATCH (n:Class) RETURN n.name, n.file LIMIT 30"})  # Graph queries

# Parse each package
abcoder parse /path/to/package --lang typescript --name package-name --output ~/abcoder-asts

get_repo_structure({repo_name: "package-name"})
get_file_structure({repo_name: "package-name", file_path: "src/core/types.ts"})
get_ast_node({repo_name: "package-name", node_ids: [{mod_path: "...", pkg_path: "...", name: "ClassName"}]})

package-a/backend    → Task 1
package-a/frontend   → Task 2
package-b/backend    → Task 3
package-b/frontend   → Task 4
cross-layer-guide    → Task 5

python3 .trellis/scripts/task.py create "Fill <package> <layer> spec" --slug <package>-<layer>-spec

# Fill <package> <layer> spec

## Goal
One sentence: what to analyze, what files to fill.

## Context
Project-specific architectural knowledge you gathered in Phase 1.
Key concepts, patterns, abstractions — everything the agent needs
to understand the codebase without reading every file.

## Tools Available
[Use the MCP Tools Template below]

## Files to Fill
List each spec file with bullet points on what to document.
Include hints about which source files to analyze.

## Important Rules

### Spec files are NOT fixed — adapt to reality
- Delete template files that don't apply
- Create new files for patterns templates don't cover
- Rename files if template names don't fit
- Update index.md to reflect the final set

### Parallel agents — stay in your lane
- ONLY modify files under your assigned spec directory
- DO NOT modify source code, other spec directories, or task files
- DO NOT run git commands
- You may read any file for analysis

## Acceptance Criteria
- [ ] Real code examples from the actual codebase (with file paths)
- [ ] Anti-patterns documented
- [ ] No placeholder text remaining
- [ ] index.md reflects actual file set

## Technical Notes
Package path, language, framework, build tools, key deps.

## Tools Available

You have two MCP servers configured — use both for accurate specs:

### GitNexus MCP (architecture-level: clusters, execution flows, impact)
| Tool | Purpose | Example |
|------|---------|---------|
| `gitnexus_query` | Find execution flows by concept | `gitnexus_query({query: "..."})` |
| `gitnexus_context` | 360-degree symbol view | `gitnexus_context({name: "ClassName"})` |
| `gitnexus_impact` | Blast radius analysis | `gitnexus_impact({target: "X", direction: "upstream"})` |
| `gitnexus_cypher` | Direct graph queries | `gitnexus_cypher({query: "MATCH ..."})` |

### ABCoder MCP (symbol-level: AST nodes, signatures, cross-file deps)
| Tool | Purpose | Example |
|------|---------|---------|
| `get_repo_structure` | Full file listing | `get_repo_structure({repo_name: "pkg"})` |
| `get_file_structure` | All nodes in a file | `get_file_structure({repo_name: "pkg", file_path: "src/..."})` |
| `get_ast_node` | Code + deps + refs | `get_ast_node({repo_name: "pkg", node_ids: [...]})` |

### Recommended Workflow
1. GitNexus first — find relevant execution flows and clusters
2. ABCoder second — get exact code patterns and signatures
3. Read source files — for full context where needed
4. Write specs — with real code examples from steps 2-3

# One terminal per task
codex -q "Read .trellis/tasks/<task-slug>/prd.md and execute the task. Use GitNexus and ABCoder MCP tools to analyze the codebase, then fill all spec files listed in the PRD."

# Line counts — 0 or ~50 means still template
find .trellis/spec -name "*.md" -exec sh -c 'echo "$(wc -l < "$1") $1"' _ {} \; | sort -rn

# Check for remaining placeholders
grep -rl "To be filled" .trellis/spec/

# Newly created or modified files
find .trellis/spec -name "*.md" -newer .trellis/tasks/ -exec ls -la {} \;