fix: server.json audit corrections + OCI ownership label

[aliasunder]

Summary

Follow-up to #55. A thorough audit of server.json against the 2025-12-11 MCP server schema, the env vars the code actually reads, the published Docker image, the GitHub repo metadata, and all four compose files.

The guiding realization: the MCP Registry path consumes server.json only — the compose files are never involved. A client pulls the OCI image and builds a docker run purely from server.json's runtimeArguments + environmentVariables + transport. So server.json must be self-sufficient, and container-internal implementation details must live in the image (Dockerfile ENV), not be exposed as phantom config knobs.

Critical fixes (the published entry would not work)

1. Dockerfile — OCI ownership label. mcp-publisher publish verifies image ownership via LABEL io.modelcontextprotocol.server.name, which must match name in server.json. Was missing.
2. packages[0].identifier — ghcr.io/aliasunder/vault-cortex → ghcr.io/aliasunder/vault-mcp. The published image is vault-mcp (see deploy.yml:22 + all compose files); the vault-cortex image never existed, so the old entry pointed at a 404.
3. repository.id — "aliasunder/vault-cortex" → "1226067541" (the numeric GitHub repo ID the schema requires).

Container internals moved to the Dockerfile (removed from server.json)

These four are hardcoded in every compose file — never user-tunable — so they're implementation details, not knobs. Each was overloaded or latently buggy when exposed in environmentVariables:

• VAULT_PATH — was both the user's host path (in -v) and the container path (env var). Now baked ENV VAULT_PATH=/vault; the only VAULT_PATH a user sees is the host side of the -v {VAULT_PATH}:/vault:rw bind mount.
• PORT — was the host port (-p {PORT}:8000) AND the container listen port (env var). Overriding it desynced them (-p 9000:8000 while the server moved to 9000 → connection refused). Now baked ENV PORT=8000; PORT survives only as the host-side mapping variable.
• HOST — overriding to 127.0.0.1 made the server unreachable through the port mapping. Now baked ENV HOST=0.0.0.0.
• INDEX_DB_PATH — hardcoded /data/index.db everywhere. Now baked ENV INDEX_DB_PATH=/data/index.db.

Final Dockerfile runtime ENV: NODE_ENV=production PORT=8000 HOST=0.0.0.0 VAULT_PATH=/vault INDEX_DB_PATH=/data/index.db.

server.json now describes the real consumer experience

• transport.headers — declares Authorization: Bearer {MCP_AUTH_TOKEN} so clients know what to send to /mcp.
• runtimeHint: "docker" + runtimeArguments — -p {PORT}:8000, -v {VAULT_PATH}:/vault:rw (bind mount, the user's vault), and -v vault-cortex-data:/data (named volume — persists search index, OAuth token DB, and logs across restarts, matching deploy/local's mcp_data:/data).
• PUBLIC_URL — isRequired: false with default: "http://localhost:8000" (the server .required()s it; the default lets the local quickstart work without manual override).
• Env-var list trimmed to the 10 genuinely user-tunable values, each with the correct default sourced from the code/compose: MCP_AUTH_TOKEN, PUBLIC_URL, MEMORY_DIR, TZ, LOG_LEVEL, LOG_DIR, LOG_RETENTION_DAYS, PROTECTED_PATHS, ORPHAN_EXCLUDE_FOLDERS, SERVICE_DOCUMENTATION_URL.
• LOG_DIR — no default (opt-in), matching the deploy/local change below. Logs go to stdout unless the user sets a path.
• Description — dropped the misleading "Remote" prefix → MCP server for Obsidian vaults — search, memory, link graph, 23 tools, OAuth-protected. (87 chars, under the 100 max). "Remote" implied a hosted URL we don't offer; the package describes a local docker run.

Compose + .env.example consistency

• All four compose files now document the runtime-derived smart defaults inline (PROTECTED_PATHS, ORPHAN_EXCLUDE_FOLDERS, SERVICE_DOCUMENTATION_URL) instead of pointing at the README.
• LOG_DIR made user-overridable in deploy/local (${LOG_DIR:-} — opt-in, file logging off by default for a quick local trial) and deploy/remote (${LOG_DIR:-/data/logs} — on by default for an unattended server). Documented in both .env.example files. Root docker-compose.yml left hardcoded (its .env.example already documents LOG_DIR as intentionally fixed for the Lightsail deploy).
• Adopter compose comment — added the upstream-fix tracker hint to deploy/remote's init-config-perms comment, mirroring the root file.

Validation

• jq schema-shape check: all required fields present at every level
• Description: 94 → 87 chars (under the 100 max)
• All 10 declared env vars verified to be env.get(NAME) / env.NAME reads in src/; the 4 removed ones (VAULT_PATH, PORT, HOST, INDEX_DB_PATH) are baked into the Dockerfile ENV
• All four compose files re-parsed as valid YAML
• 496 / 496 tests pass; lint + tsc --noEmit clean; prettier clean

⚠️ Hard gate before registry submission: cut v0.15.4 first

server.json on this branch only works against an image built from this branch's Dockerfile. The released v0.15.3 image bakes only PORT + HOST — not VAULT_PATH/INDEX_DB_PATH. Since VAULT_PATH is .required() (server.ts:35) and is no longer in server.json, a container spawned from this server.json against the v0.15.3 image would crash on startup.

Required order:

1. Merge this PR
2. Cut v0.15.4 via Manual Release — rebuilds the image with the new Dockerfile ENV and bumps packages[0].version → 0.15.4
3. Then mcp-publisher publish — now the registry references the v0.15.4 image that has the bakes

Sources:

• MCP server.json schema 2025-12-11
• MCP Registry — Supported Package Types
• GoReleaser MCP publish docs (OCI label syntax)
• github-mcp-server server.json