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biblio: New biblio_compile tool

Goal

(promoted from note)

Context

(see source note)

Prompt

Fix the issue described below (source: docs/log/issue/issue-arash-20260402-220152-539138.md). Understand the problem, then implement the proposed fix.

biblio: New biblio_compile tool — merge intermediates into compiled.bib

New function in packages/biblio/src/biblio/bibtex.py:

def compile_bib(sources: list[Path], output: Path, *, dry_run: bool = False) -> tuple[int, int]:
    """Merge multiple .bib intermediates into a single compiled output.

    Reuses pybtex merge logic. Duplicate keys across sources use last-wins.
    Returns (n_sources, n_entries).
    """

Config in render.yml (read by projio):

bibliography: .projio/render/compiled.bib
bib_sources:
  - .projio/biblio/merged.bib
  - .projio/pipeio/modkey.bib

MCP tool in packages/biblio/src/biblio/mcp.py:

  • mcp_biblio_compile(root, sources=None, output=None)
  • If sources not given, reads from render.yml bib_sources
  • If output not given, reads from render.yml bibliography
  • Skips missing source files gracefully (pipeio might not exist in all projects)

MCP registration in src/projio/mcp/biblio.py:

  • Register biblio_compile tool that wraps the biblio function
  • Reads render.yml for default config

Workflow integration:

  • projio sync calls: biblio_merge → modkey_bib (if pipeio present) → biblio_compile
  • Both pandoc (via pandoc-defaults.yaml) and mkdocs (via bib_file config) point to .projio/render/compiled.bib
  • issue-arash-20260402-220025-468258.md — Spec for the new bib architecture (sources vs artifacts separation) that biblio_compile implements — compiled.bib is the artifact, merged.bib/modkey.bib are the sources
  • issue-arash-20260402-220130-159401.md — About moving biblio merge output and config to a new location — directly affects the merged.bib source path that biblio_compile reads
  • issue-arash-20260402-220100-339672.md — About changing modkey.bib (pipeio modkey) — modkey.bib is one of the bib_sources that biblio_compile merges into compiled.bib

Acceptance Criteria

  • [ ]

Result

(pending)

Batch Result

  • status: done
  • batch queue_id: 9ef168fb767a
  • session: 5770b78c-f4c8-4794-9f73-aedd6692dafa
  • batch duration: 1363.6s