Refactor/yaml target manifests

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here.
+
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.4.0] - 2026-05-22
+
+> Breaking release. Target manifests and `agpack.yml` were overhauled to make every resource generic. The old MCP-specific syntax has no in-place upgrade — see the migration block below.
+
+### Added
+
+- **YAML target manifests + `target_definitions:` in `agpack.yml`.** Built-in targets (Claude, Cursor, Gemini, Codex, OpenCode, Copilot) now ship as YAML manifests; users can define or override targets directly in `agpack.yml`. New CLI: `agpack targets list` and `agpack targets show <name>`.
+- **Three resource kinds: `copy-directory`, `copy-file`, `edit-file`.** Declared per resource as `kind:` + `path:`. Per-kind logic lives in `agpack.kinds`; the deployer is a thin orchestrator.
+- **Generic `edit-file` for any JSON/TOML config**, not just MCP. Patches are `{key, value, strategy: replace | append}` under `dependencies:`. The engine walks the dotted `key`, auto-creates intermediates, and on cleanup reverses replaces by key and appends by deep-equality match (no markers in user files). The built-in `claude` target ships an `edit-file` resource for `.claude/settings.json` (hooks/permissions) alongside `mcp`.
+- **Per-target `vars:` with `${name}` substitution in patches.** Each target manifest declares a `vars:` map (e.g. `bucket: mcpServers` for Claude, `mcp` for OpenCode, `mcp_servers` for Codex). One patch `key: ${bucket}.filesystem` deploys correctly everywhere. Target vars take precedence over env vars on collision.
+- **Open resource taxonomy.** `skills`, `commands`, `agents`, `mcp` are conventions used by the built-ins — any string is a valid resource-type name in both `dependencies:` and `target_definitions`.
+
+### Changed
+
+- Configuration errors now raise structured exceptions instead of failing late during deploy.
+- Logging no longer echoes secrets pulled from `env:` substitutions.
+
+### Removed
+
+- The MCP-specific encoder (`McpServer`, transport-aware encoding, `merge: {servers_key, defaults, transports}`). Per-target quirks are now explicit patches.
+- `format:` on edit-file resources (inferred from path extension).
+- `layout: directory | file` on copy resources (replaced by `kind: copy-directory | copy-file`).
+
+### Migration from 0.3.x
+
+Old `agpack.yml`:
+
+```yaml
+dependencies:
+  mcp:
+    - name: filesystem
+      command: npx
+      args: ["-y", "@modelcontextprotocol/server-filesystem", "."]
+      env:
+        API_KEY: ${API_KEY}
+```
+
+New `agpack.yml`:
+
+```yaml
+dependencies:
+  mcp:
+    - key: ${bucket}.filesystem         # resolves per-target via vars
+      value:
+        command: npx
+        args: ["-y", "@modelcontextprotocol/server-filesystem", "."]
+        env:
+          API_KEY: ${API_KEY}
+```
+
+`${bucket}` resolves per target from each built-in's `vars:`: `mcpServers` for Claude/Cursor/Gemini, `mcp_servers` for Codex, `mcp` for OpenCode, `servers` for Copilot.
+
+For custom `target_definitions:`, drop the `merge:` block and `format:` from edit-file resources, replace `layout: directory|file` with `kind: copy-directory|copy-file`, and add `vars: { bucket: <key> }` on edit-file resources whose patches use `${bucket}.<name>`.
+
+**Lockfile:** the format changed and agpack does not read pre-release lockfiles — delete `.agpack.lock.yml` before the first sync. Legacy singular resource-type keys (`skill`/`command`/`agent`) are remapped to plural on read, so cleanup of older lockfiles still works.
+
+## [0.3.1] - 2026-04-05
+
+### Added
+
+- Multiple URLs per dependency: `url:` accepts a list, tried in order (e.g. HTTPS primary with SSH fallback). The first URL is canonical for identity and display.
+
+## [0.3.0] - 2026-04-05
+
+### Added
+
+- Global config at `~/.config/agpack/agpack.yml` for dependencies and MCP servers shared across projects.
+- Per-project opt-out via `global: false` in `agpack.yml`, or `agpack sync --no-global` from the CLI.
+- Project dependencies and MCP servers win on conflict when merged with the global config.
+
+## [0.2.1] - 2026-03-26
+
+### Changed
+
+- Improved progress / status styling.
+
+## [0.2.0] - 2026-03-26
+
+### Added
+
+- Folder-of-skills support: a dependency `path` pointing at a directory of subfolders expands to one skill per subfolder.
+
+## [0.1.7] - 2026-03-26
+
+### Fixed
+
+- Added a proper timeout for `git fetch` operations and disabled interactive git prompts so a stalled clone can no longer hang sync indefinitely (#2).
+
+## [0.1.6] - 2026-03-25
+
+### Added
+
+- `${VAR}` env-variable substitution in MCP server `env:` and other config values, resolved from `.env` or the shell environment.
+
+## [0.1.5] - 2026-03-23
+
+### Added
+
+- MCP server config merging into each tool's project-level config file.
+
+### Changed
+
+- User-feedback improvements during sync (status / progress output).
+
+### Fixed
+
+- Type-check failures and CI configuration.
+
+[Unreleased]: https://github.com/PhilippTh/agpack/compare/v0.4.0...HEAD
+[0.4.0]: https://github.com/PhilippTh/agpack/compare/v0.3.1...v0.4.0
+[0.3.1]: https://github.com/PhilippTh/agpack/compare/v0.3.0...v0.3.1
+[0.3.0]: https://github.com/PhilippTh/agpack/compare/v0.2.1...v0.3.0
+[0.2.1]: https://github.com/PhilippTh/agpack/compare/v0.2.0...v0.2.1
+[0.2.0]: https://github.com/PhilippTh/agpack/compare/v0.1.7...v0.2.0
+[0.1.7]: https://github.com/PhilippTh/agpack/compare/v0.1.6...v0.1.7
+[0.1.6]: https://github.com/PhilippTh/agpack/compare/v0.1.5...v0.1.6
+[0.1.5]: https://github.com/PhilippTh/agpack/releases/tag/v0.1.5