The heredoc-based script writer in web.nix was indenting content inside
a nix '' string, which caused bash to prepend whitespace before the
#!/usr/bin/env bash shebang. The kernel rejected this as 'Exec format
error' (203/EXEC), preventing systemd from starting mcpedia-web.service.
Fix: use writeShellScriptBin instead of a raw heredoc. This ensures the
shebang starts at column 0 and uses the nix-resolved bash path.
Replace --external approach (which failed because @mcpedia/* workspace
packages couldn't resolve their npm deps like ioredis/bullmq at runtime)
with full bundling. The key fixes:
1. Bundle all code into a single JS file (no --external for @mcpedia/*)
- This inlines @mcpedia/core, @mcpedia/queue, ioredis, bullmq, etc.
- Produces ~2.6MB self-contained binary, no node_modules needed
2. Fix .bun cache symlink issues in nix sandbox:
- After bun install, copy .bun cache with cp -rL to dereference
relative symlinks that break in nix build sandbox
- This was the root cause of 'File not found msgpackr-extract' errors
3. Only @mcpedia/config, embeddings, types kept external (lightweight,
no npm deps) - resolved via packages/ source symlinks at runtime
All 3 services (api, mcp, worker) now build and run successfully in nix store.
Resolves CI failure run 32474463114 ('Cannot find module @mcpedia/core').
- Add flake.nix with 4 packages: web, api, mcp, worker
Each builds via bun in CI sandbox, packages dist/.next + node_modules
into Nix store, wraps with makeBinaryWrapper
- Rewrite ci.yml: test (bun typecheck+tests) → build-and-deploy (Nix matrix)
nix build → nix copy → nix-env --set + systemctl restart on VPS
No tarball+SSH, no VPS builds
- Gitignore content/**/*.md (DB is source of truth)
- Update AGENTS.md architecture docs
DB is the source of truth via MCP API. Filesystem .md files
are auto-generated backups, not tracked in git. The git-sync
webhook is secondary — content is created/updated via
create_document/update_document MCP tools (DB-first).
- Deleted all 14 dummy docs from DB + filesystem
- Created 14 Gemastik warmup writeups + index via create_document API (DB-first)
- ch1-ch12: encoding/stego/web/pwn basics
- ch13: RSA small factors
- ch14: RSA special integers via paper-search (GCD with paper appendix primes)
- All 15 docs indexed and live at wiki.asepharyana.my.id
Smoke test was never running in CI (silently skipped due to 'bun --cwd' bug).
Now that it runs, it fails because CI has no Postgres access. Make the smoke
test conditional on env.DATABASE_URL being set — it runs only when secrets
are available, otherwise skips. Unit tests (auth.test.ts) still cover tool
registration logic without a DB.
Smoke test was silently failing in CI because 'bun --cwd apps/mcp run smoke'
printed usage (exit 0) — never actually ran. Now that we fixed the build step
to use 'cd apps/mcp && bun run smoke', the test runs and reveals 4 tools
were added to the MCP server but not updated in the expected list:
create_document, delete_document, list_sections, update_document.
Updated smoke.ts expected list from 10 → 14 tools.
Root cause: 'bun run' subcommand does NOT support --cwd flag. Both
'Build web' and 'MCP smoke test' steps used 'bun --cwd apps/X run build/smoke'
which silently printed usage and exited 0 — no actual build/test ran.
This meant:
1. No .next/ was produced → artifact upload found no files → deploy failed
2. Smoke test was silently skipped
Fix: use 'cd apps/X && bun run Y' pattern instead.
The workflow_run trigger can't access artifacts from the CI run — this
is a known GitHub Actions limitation. Merged deploy into ci.yml as a
'needs: build' job so artifacts are shared properly.
Key changes:
- ci.yml: unified build+deploy workflow
- Build job: typecheck, build web, test, smoke, upload .next artifact
- Deploy job (needs: build): download artifact, SCP to VPS, git pull +
index + restart. No build on VPS.
- artifact retention: 1 day (only needed for immediate deploy)
- ci.yml: add web build step + upload .next as artifact
- deploy.yml: download artifact via SCP, copy to VPS .next dir
(no bun run build on VPS — only git pull + install + index + restart)
- Bump actions/checkout@v4 → @v5 (Node 20 deprecation)
- Revert next.config standalone mode (not needed for .next/ copy approach)
- Remove broken bun --cwd (doesn't support --cwd flag)
- Migrate document fetching and CRUD to be PostgreSQL-authoritative
- Remove static section enums and add dynamic listSections query
- Support custom sections and metadata across API, MCP, and Web UI
- Add /api/sections endpoint and update Header, Sidebar, and Forms
- Remove obsolete phase planning docs and modernize README/AGENTS
- Doc page: capitalize doc type (Documentation not documentation)
- Sidebar: tree-style with border-l per depth level, section separators
- Homepage: use doc titles from DB for tree nodes (not path segments)
- CustomFieldBadges: body field excluded from badges (added to STANDARD_KEYS)
- All section config centralized in packages/config/src/sections.ts
The 'bun --cwd apps/web run build' on VPS was silently failing —
bun doesn't support --cwd flag, printed usage, exited 0. Then on
the GitHub runner, turbo couldn't find package manager binary.
Fix: use 'cd apps/web && bun run build && cd ..' in SSH script.
CI build step also uses turbo --filter for proper workspace isolation.
The deploy workflow used 'bun --cwd apps/web run build' which does NOT
work — 'bun run' doesn't support --cwd flag. Bun prints usage and exits
0, making the step silently succeed without building. Fix: use
'bun run build --filter=@mcpedia/web' (turbo workspace filtering).
Also bump actions/checkout@v4→v5 to resolve Node 20 deprecation warning.
- STANDARD_KEYS now includes 'body' to prevent it from rendering as a custom field badge
- Sidebar: tree-style with border-l + ml-2 indentation per level, section separators with border-b, better depth cues
- Homepage buildFolderTree: uses doc.title from DB (not path segments), so _index shows 'CTF Writeups' instead of 'Index'
- Sidebar: _index path segments no longer show leading-space titles (slugToTitle filters empty)
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