feat: initial project scaffold

pyproject.toml (Python 3.12, uv), codex/ package (config, db, models),
infra/ (docker-compose + schema), .env.example, .gitignore, README.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

codex/models.py

@@ -0,0 +1,80 @@
+"""Domain dataclasses.
+
+Each class maps directly to a table in ``infra/schema.sql``.
+Field names and types are kept in sync with the DDL.
+
+All fields that are nullable in the schema are typed as ``… | None``
+with a default of ``None`` so instances can be constructed incrementally.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from datetime import datetime
+
+
+@dataclass
+class Paper:
+    """Maps to the ``papers`` table (Layer 1 — semantic search).
+
+    ``id`` is the canonical identifier: an arXiv ID (e.g. ``2301.00001``)
+    or a DOI (e.g. ``10.1145/3592430``).
+    """
+
+    id: str
+    title: str
+    openalex_id: str | None = None
+    bibkey: str | None = None
+    authors: list[str] = field(default_factory=list)
+    year: int | None = None
+    abstract: str | None = None
+    source_path: str | None = None
+    # abstract_emb is a list of floats representing the pgvector column;
+    # pgvector's Python driver accepts list[float] for vector columns.
+    abstract_emb: list[float] | None = None
+    added_at: datetime | None = None
+
+
+@dataclass
+class Chunk:
+    """Maps to the ``chunks`` table (Layer 1 — full-text chunks).
+
+    ``id`` is set by the database (BIGSERIAL); leave it as ``None``
+    when constructing a new chunk before insertion.
+    """
+
+    paper_id: str
+    ord: int
+    content: str
+    id: int | None = None
+    embedding: list[float] | None = None
+
+
+@dataclass
+class Citation:
+    """Maps to the ``citations`` table (Layer 2 — citation graph).
+
+    ``cited_id`` intentionally has no foreign-key constraint in the schema;
+    citations to not-yet-ingested papers are preserved as discovery leads.
+    """
+
+    citing_id: str
+    cited_id: str
+    context: str | None = None
+
+
+@dataclass
+class CodeLink:
+    """Maps to the ``code_links`` table (Layer 3 — provenance).
+
+    ``symbol`` is a C++ qualified name or ``file.cpp:line`` reference.
+    ``role`` is a free-text description such as 'implements Thm 3.2'.
+    ``id`` is set by the database (BIGSERIAL).
+    """
+
+    symbol: str
+    paper_id: str | None = None
+    role: str | None = None
+    note: str | None = None
+    id: int | None = None
+    added_at: datetime | None = None