Feature/headless agent layer

[dannydoor]

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Pull request overview

This PR introduces a new mcp/ subtree that packages Foldseek Server capabilities as an MCP server for headless/agent use, including deterministic build artifacts and a release workflow, while also refactoring shared frontend helpers into standalone modules.

Changes:

• Add mcp/core (private library) and mcp/server (MCP server) with schemas, artifact resources, local input handling, and extensive offline tests.
• Add deterministic packaging scripts for a minimal plugin runtime and a Desktop .mcpb bundle, plus a GitHub Actions release workflow.
• Refactor/move several frontend helpers into frontend/lib/* modules and build tooling (frontend/build-tools/*), removing the previous page-global “resultsApi” surface.

File summaries

File	Description
mcp/server/test/transport.test.js	Adds transport/HTTP/security contract tests for the MCP server.
mcp/server/test/surface.test.js	Verifies the advertised MCP tool surface and stable error codes.
mcp/server/test/resources.test.js	Tests artifact resource listing/reading and traversal/size protections.
mcp/server/test/release.test.js	Ensures release graph isolation and manifest/tool parity.
mcp/server/test/plugin-runtime.test.js	Verifies deterministic plugin-runtime zip build and tool surface.
mcp/server/test/inputs.test.js	Tests allowlisted local file inputs and refusal cases.
mcp/server/src/resources.js	Implements artifact resource listing and bounded reads.
mcp/server/package.json	Defines the MCP server package, deps, and test/build scripts.
mcp/server/pack-plugin-runtime.mjs	Builds a minimal, self-contained runtime zip via esbuild + licenses.
mcp/server/pack-mcpb.mjs	Builds a Claude Desktop .mcpb bundle from the same runtime.
mcp/server/manifest.json	Desktop manifest describing tools and configuration.
mcp/server/build.mjs	Bundles server + core for release artifacts.
mcp/server/bin/foldseek-server-mcp.js	Entry point selecting source vs bundled runtime and argv/env handling.
mcp/server/.mcpbignore	Excludes dev-only files from Desktop bundle packaging.
mcp/README.md	Documents the new mcp/ packages, quick start, and test expectations.
mcp/core/test/schemas.test.js	Adds/extends schema validation tests for summaries and artifacts.
mcp/core/test/artifact-gc.test.js	Adds tests for GC behavior, symlink safety, and result cache cleanup.
mcp/core/src/taxonomy.js	Adds taxonomy-name resolution and filter parsing/inspection helpers.
mcp/core/src/summary.js	Adds bounded “result summary” generation with validation.
mcp/core/src/submit.js	Adds forwarding/submission builders for different destinations.
mcp/core/src/structures.js	Adds structure fetching/reconstruction helpers and accession loading.
mcp/core/src/store.js	Implements filesystem state store for tickets/results/selections.
mcp/core/src/schemas.js	Defines public contract schemas + validators.
mcp/core/src/results.js	Adds result table/row/selection helpers and forwarding integration.
mcp/core/src/motif.js	Adds motif parsing/validation and chain normalization logic.
mcp/core/src/metrics.js	Adds metric semantics and default ranking/sorting helpers.
mcp/core/src/inputs.js	Adds allowlisted local input path resolution + shared dir management.
mcp/core/src/index.js	Exposes core library surface and re-exports shared frontend helpers.
mcp/core/src/facts.js	Adds pure helpers for identity/counts/completeness/provenance/serialization.
mcp/core/README.md	Documents responsibilities, layout, and offline testing for core.
mcp/core/package.json	Defines the private core package and its export entry.
frontend/webpack.frontend.config.js	Updates PO tooling paths and babel-loader roots for the refactor.
frontend/SendToMixin.vue	Removes the old send-to mixin implementation.
frontend/Search.vue	Removes SearchApi mixin usage.
frontend/ResultFoldseekDB.vue	Removes large inline explanatory comments (functional logic unchanged here).
frontend/ResultFoldMason.vue	Removes API augmentation/sending code tied to the deleted page API.
frontend/ResultFoldDiscoDB.vue	Removes large inline explanatory comments (functional logic unchanged here).
frontend/Queue.vue	Removes queue page API registration code tied to the deleted page API.
frontend/MultimerSearch.vue	Removes SearchApi mixin usage.
frontend/lib/vue-simple-portal/index.js	Adds explicit .js extensions for ESM compatibility.
frontend/lib/vue-simple-portal/components/Portal.js	Adds explicit .js extensions for ESM compatibility.
frontend/lib/ticketRoute.js	Trims comment blocks while keeping routing helpers.
frontend/lib/taxonomyFilter.js	Trims comment blocks while keeping subtree expansion logic.
frontend/lib/targetName.js	New helper module extracted from Utilities for accession/chain parsing.
frontend/lib/resultSort.js	Trims comment blocks; keeps shared sorting helpers.
frontend/lib/resultsApi.js	Removes the global page API registry module.
frontend/lib/pdbAssembly.js	New helper module extracted from Utilities for PDB assembly operations.
frontend/lib/package.json	Marks frontend/lib as ESM with sideEffects disabled.
frontend/lib/hitId.js	New helper module for canonical hit id normalization/splitting.
frontend/lib/alignmentColumns.js	New helper module for alignment-column ↔ residue mapping.
frontend/lib/accession.js	Switches accession fetching to fetch and expands Q-BioLiP mapping outputs.
frontend/lib/.babelrc	Adds a .babelrc to extend the parent config for the ESM lib subtree.
frontend/FoldMasonSearch.vue	Removes page API surface code tied to deleted resultsApi.
frontend/FoldDiscoSearch.vue	Removes SearchApi mixin + Q-BioLiP API surface code tied to deleted resultsApi.
frontend/build-tools/po-reader.js	Adds PO parser implementation under build-tools.
frontend/build-tools/po-loader.js	Adds PO webpack loader under build-tools.
.gitignore	Adds ignores for MCP server dist artifacts and (currently) all *.md.
.github/workflows/mcp-release.yml	Adds a workflow to test/build and optionally publish immutable MCP runtime assets.

Review details

Files not reviewed (1)

• mcp/server/package-lock.json: Generated file

• Files reviewed: 73/79 changed files
• Comments generated: 3
• Review effort level: Lite

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