refactor: move project manager to service layer (#68)

* refactor(project): manager talks to the sqlite store; drop the in-memory store

The project Manager now runs only against the durable backend store: remove the
process-local MemoryStore (and NewMemoryManager), and require a real Store. The
daemon already wires the sqlite store; tests now build a real temp-dir sqlite
store instead of the mock.

- Move Row + the Store port to project/store.go. The Store interface stays
  because it is the dependency-inversion port that lets the manager reach the
  backend without an import cycle (storage imports project.Row), not an extra
  mock layer — there is no longer any in-memory implementation.
- NewManager requires a non-nil Store (no in-memory fallback).
- Add project/manager_test.go: List/Add/Get/Remove happy paths +
  PATH_REQUIRED/NOT_A_GIT_REPO/PATH_ALREADY_REGISTERED/ID_ALREADY_REGISTERED,
  PROJECT_NOT_FOUND/INVALID_PROJECT_ID, and UpdateConfig — all against a real
  sqlite store (the service-logic tests #47 lacked).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* refactor(project): trim routes, consolidate package, add code-first OpenAPI

- Remove POST /reload, PATCH /{id}, POST /{id}/repair routes and their
  Manager methods (Reload, UpdateConfig, Repair) and DTOs (ReloadResult,
  UpdateConfigInput) — not needed at this stage
- Merge Manager interface into manager.go; delete project.go (single-impl
  split served no purpose)
- Remove dead notImplemented helper from errors.go
- Port PR #59 code-first OpenAPI generation: controllers/dto.go named
  response types, specgen/build.go (4 routes), parity + drift tests,
  cmd/genspec, go generate wiring; regenerate openapi.yaml
- Add swaggest deps; add YAML() method to apispec.Spec

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

* fix(project): address PR review comments

- t.Skipf → t.Fatalf in gitRepo helper: git failures now hard-fail
  instead of silently skipping manager tests on a misconfigured runner
- FindProjectByPath: add AND archived_at IS NULL so archived paths don't
  permanently block re-registration (update queries/projects.sql and
  generated gen/projects.sql.go)
- Add TestManager_ReaddAfterRemove to lock the fix

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

* fixed lint and fmt

* addressed greptile comments

* Apply suggestions from code review

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* project tests fix

* project_tests fix

* fix: Linting and formatting fix

* refactor: move project manager into service layer (#68)

* refactor: split service package by resource (#68)

* fix: ignore archived project id conflicts (#68)

* refactor: move pr manager into service layer (#68)

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
Co-authored-by: itrytoohard <ayetrytoohard@gmail.com>

Author: 4 people

backend/cmd/genspec/main.go

@@ -0,0 +1,26 @@
+// Command genspec writes the code-first OpenAPI document produced by
+// apispec.Build() to disk. It is invoked via `go generate` (see
+// internal/httpd/apispec/gen.go); the output openapi.yaml is committed and
+// embedded by the apispec package.
+package main
+
+import (
+	"flag"
+	"log"
+	"os"
+
+	"github.com/aoagents/agent-orchestrator/backend/internal/httpd/apispec/specgen"
+)
+
+func main() {
+	out := flag.String("out", "openapi.yaml", "output path for the generated OpenAPI document")
+	flag.Parse()
+
+	doc, err := specgen.Build()
+	if err != nil {
+		log.Fatalf("genspec: build openapi: %v", err)
+	}
+	if err := os.WriteFile(*out, doc, 0o600); err != nil {
+		log.Fatalf("genspec: write %s: %v", *out, err)
+	}
+}

backend/go.mod

@@ -8,6 +8,8 @@ require (
 	github.com/go-chi/chi/v5 v5.1.0
 	github.com/pressly/goose/v3 v3.27.1
 	github.com/spf13/cobra v1.10.1
+	github.com/swaggest/jsonschema-go v0.3.79
+	github.com/swaggest/openapi-go v0.2.61
 	golang.org/x/sys v0.43.0
 	gopkg.in/yaml.v3 v3.0.1
 	modernc.org/sqlite v1.51.0
@@ -23,8 +25,10 @@ require (
 	github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec // indirect
 	github.com/sethvargo/go-retry v0.3.0 // indirect
 	github.com/spf13/pflag v1.0.9 // indirect
+	github.com/swaggest/refl v1.4.0 // indirect
 	go.uber.org/multierr v1.11.0 // indirect
 	golang.org/x/sync v0.20.0 // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
 	modernc.org/libc v1.72.3 // indirect
 	modernc.org/mathutil v1.7.1 // indirect
 	modernc.org/memory v1.11.0 // indirect

backend/go.sum

@@ -1,3 +1,7 @@
+github.com/bool64/dev v0.2.43 h1:yQ7qiZVef6WtCl2vDYU0Y+qSq+0aBrQzY8KXkklk9cQ=
+github.com/bool64/dev v0.2.43/go.mod h1:iJbh1y/HkunEPhgebWRNcs8wfGq7sjvJ6W5iabL8ACg=
+github.com/bool64/shared v0.1.5 h1:fp3eUhBsrSjNCQPcSdQqZxxh9bBwrYiZ+zOKFkM0/2E=
+github.com/bool64/shared v0.1.5/go.mod h1:081yz68YC9jeFB3+Bbmno2RFWvGKv1lPKkMP6MHJlPs=
 github.com/coder/websocket v1.8.14 h1:9L0p0iKiNOibykf283eHkKUHHrpG7f65OE3BhhO7v9g=
 github.com/coder/websocket v1.8.14/go.mod h1:NX3SzP+inril6yawo5CQXx8+fk145lPDC6pumgx0mVg=
 github.com/cpuguy83/go-md2man/v2 v2.0.6/go.mod h1:oOW0eioCTA6cOiMLiUPZOpcVxMig6NIQQ7OS05n1F4g=
@@ -15,6 +19,8 @@ github.com/google/uuid v1.6.0 h1:NIvaJDMOsjHA8n1jAhLSgzrAzy1Hgr+hNrb57e+94F0=
 github.com/google/uuid v1.6.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
 github.com/hashicorp/golang-lru/v2 v2.0.7 h1:a+bsQ5rvGLjzHuww6tVxozPZFVghXaHOwFs4luLUK2k=
 github.com/hashicorp/golang-lru/v2 v2.0.7/go.mod h1:QeFd9opnmA6QUJc5vARoKUSoFhyfM2/ZepoAG6RGpeM=
+github.com/iancoleman/orderedmap v0.3.0 h1:5cbR2grmZR/DiVt+VJopEhtVs9YGInGIxAoMJn+Ichc=
+github.com/iancoleman/orderedmap v0.3.0/go.mod h1:XuLcCUkdL5owUCQeF2Ue9uuw1EptkJDkXXS7VoV7XGE=
 github.com/inconshreveable/mousetrap v1.1.0 h1:wN+x4NVGpMsO7ErUn/mUI3vEoE6Jt13X2s0bqwp9tc8=
 github.com/inconshreveable/mousetrap v1.1.0/go.mod h1:vpF70FUmC8bwa3OWnCshd2FqLfsEA9PFc4w1p2J65bw=
 github.com/mattn/go-isatty v0.0.21 h1:xYae+lCNBP7QuW4PUnNG61ffM4hVIfm+zUzDuSzYLGs=
@@ -30,6 +36,8 @@ github.com/pressly/goose/v3 v3.27.1/go.mod h1:maruOxsPnIG2yHHyo8UqKWXYKFcH7Q76cs
 github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec h1:W09IVJc94icq4NjY3clb7Lk8O1qJ8BdBEF8z0ibU0rE=
 github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec/go.mod h1:qqbHyh8v60DhA7CoWK5oRCqLrMHRGoxYCSS9EjAz6Eo=
 github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
+github.com/sergi/go-diff v1.3.1 h1:xkr+Oxo4BOQKmkn/B9eMK0g5Kg/983T9DqqPHwYqD+8=
+github.com/sergi/go-diff v1.3.1/go.mod h1:aMJSSKb2lpPvRNec0+w3fl7LP9IOFzdc9Pa4NFbPK1I=
 github.com/sethvargo/go-retry v0.3.0 h1:EEt31A35QhrcRZtrYFDTBg91cqZVnFL2navjDrah2SE=
 github.com/sethvargo/go-retry v0.3.0/go.mod h1:mNX17F0C/HguQMyMyJxcnU471gOZGxCLyYaFyAZraas=
 github.com/spf13/cobra v1.10.1 h1:lJeBwCfmrnXthfAupyUTzJ/J4Nc1RsHC/mSRU2dll/s=
@@ -38,6 +46,18 @@ github.com/spf13/pflag v1.0.9 h1:9exaQaMOCwffKiiiYk6/BndUBv+iRViNW+4lEMi0PvY=
 github.com/spf13/pflag v1.0.9/go.mod h1:McXfInJRrz4CZXVZOBLb0bTZqETkiAhM9Iw0y3An2Bg=
 github.com/stretchr/testify v1.11.1 h1:7s2iGBzp5EwR7/aIZr8ao5+dra3wiQyKjjFuvgVKu7U=
 github.com/stretchr/testify v1.11.1/go.mod h1:wZwfW3scLgRK+23gO65QZefKpKQRnfz6sD981Nm4B6U=
+github.com/swaggest/assertjson v1.9.0 h1:dKu0BfJkIxv/xe//mkCrK5yZbs79jL7OVf9Ija7o2xQ=
+github.com/swaggest/assertjson v1.9.0/go.mod h1:b+ZKX2VRiUjxfUIal0HDN85W0nHPAYUbYH5WkkSsFsU=
+github.com/swaggest/jsonschema-go v0.3.79 h1:0TOShCbAJ9Xjt1e2W83l+QtMQSG2pbun2EkiYTyafCs=
+github.com/swaggest/jsonschema-go v0.3.79/go.mod h1:GqVmJ+XNLeUHhFIhHNKc+C68euxfrl3a3aoZH4vTRl0=
+github.com/swaggest/openapi-go v0.2.61 h1:psc+LE7pWhEjmJpmkti9tUmBPkkobdUNflBf5Ps6JSc=
+github.com/swaggest/openapi-go v0.2.61/go.mod h1:786CwSwleh1IorB0nfwYGESWf83JgQh6fBc1PeJe4Iw=
+github.com/swaggest/refl v1.4.0 h1:CftOSdTqRqs100xpFOT/Rifss5xBV/CT0S/FN60Xe9k=
+github.com/swaggest/refl v1.4.0/go.mod h1:4uUVFVfPJ0NSX9FPwMPspeHos9wPFlCMGoPRllUbpvA=
+github.com/yudai/gojsondiff v1.0.0 h1:27cbfqXLVEJ1o8I6v3y9lg8Ydm53EKqHXAOMxEGlCOA=
+github.com/yudai/gojsondiff v1.0.0/go.mod h1:AY32+k2cwILAkW1fbgxQ5mUmMiZFgLIV+FBNExI05xg=
+github.com/yudai/golcs v0.0.0-20170316035057-ecda9a501e82 h1:BHyfKlQyqbsFN5p3IfnEUduWvb9is428/nNb5L3U01M=
+github.com/yudai/golcs v0.0.0-20170316035057-ecda9a501e82/go.mod h1:lgjkn3NuSvDfVJdfcVVdX+jpBxNmX4rDAzaS45IcYoM=
 go.uber.org/multierr v1.11.0 h1:blXXJkSxSSfBVBlC76pxqeO+LN3aDfLQo+309xJstO0=
 go.uber.org/multierr v1.11.0/go.mod h1:20+QtiLqy0Nd6FdQB9TLXag12DsQkrbs3htMFfDN80Y=
 golang.org/x/mod v0.33.0 h1:tHFzIWbBifEmbwtGz65eaWyGiGZatSrT9prnU8DbVL8=
@@ -50,6 +70,8 @@ golang.org/x/tools v0.42.0 h1:uNgphsn75Tdz5Ji2q36v/nsFSfR/9BRFvqhGBaJGd5k=
 golang.org/x/tools v0.42.0/go.mod h1:Ma6lCIwGZvHK6XtgbswSoWroEkhugApmsXyrUmBhfr0=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
+gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
 gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
 gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 modernc.org/cc/v4 v4.28.2 h1:3tQ0lf2ADtoby2EtSP+J7IE2SHwEJdP8ioR59wx7XpY=

backend/internal/adapters/scm/github/doc.go

@@ -114,7 +114,7 @@
 //
 //   - The poller loop and cadence selection (issue #35).
 //   - Webhook ingestion (this package is polling-only).
-//   - Persistence (PR Manager owns the row mapping; see internal/pr).
+//   - Persistence (PR Manager owns the row mapping; see internal/service/pr).
 //   - Linear / GitLab providers (separate PRs).
 //   - Issue tracking (separate lane, see internal/adapters/tracker).
 //   - Comment-injection-into-session-context (Messenger lane, not SCM).

backend/internal/cdc/cdc_test.go

@@ -9,7 +9,6 @@ import (
 
 	"github.com/aoagents/agent-orchestrator/backend/internal/cdc"
 	"github.com/aoagents/agent-orchestrator/backend/internal/domain"
-	"github.com/aoagents/agent-orchestrator/backend/internal/project"
 	"github.com/aoagents/agent-orchestrator/backend/internal/storage/sqlite"
 )
 
@@ -27,7 +26,7 @@ func seedSession(t *testing.T, s *sqlite.Store) domain.SessionRecord {
 	t.Helper()
 	ctx := context.Background()
 	now := time.Now().UTC().Truncate(time.Second)
-	if err := s.Upsert(ctx, project.Row{ID: "mer", Path: "/m", RegisteredAt: now}); err != nil {
+	if err := s.UpsertProject(ctx, domain.ProjectRecord{ID: "mer", Path: "/m", RegisteredAt: now}); err != nil {
 		t.Fatal(err)
 	}
 	r, err := s.CreateSession(ctx, domain.SessionRecord{

backend/internal/daemon/daemon.go

@@ -14,8 +14,8 @@ import (
 	"github.com/aoagents/agent-orchestrator/backend/internal/adapters/runtime/zellij"
 	"github.com/aoagents/agent-orchestrator/backend/internal/config"
 	"github.com/aoagents/agent-orchestrator/backend/internal/httpd"
-	"github.com/aoagents/agent-orchestrator/backend/internal/project"
 	"github.com/aoagents/agent-orchestrator/backend/internal/runfile"
+	projectsvc "github.com/aoagents/agent-orchestrator/backend/internal/service/project"
 	"github.com/aoagents/agent-orchestrator/backend/internal/storage/sqlite"
 	"github.com/aoagents/agent-orchestrator/backend/internal/terminal"
 )
@@ -66,7 +66,7 @@ func Run() error {
 	termMgr := terminal.NewManager(runtimeAdapter, cdcPipe.Broadcaster, log)
 	defer termMgr.Close()
 
-	srv, err := httpd.NewWithDeps(cfg, log, termMgr, httpd.APIDeps{Projects: project.NewManager(store)})
+	srv, err := httpd.NewWithDeps(cfg, log, termMgr, httpd.APIDeps{Projects: projectsvc.New(store)})
 	if err != nil {
 		stop()
 		if cdcErr := cdcPipe.Stop(); cdcErr != nil {

backend/internal/daemon/wiring_test.go

@@ -10,7 +10,6 @@ import (
 	"github.com/aoagents/agent-orchestrator/backend/internal/domain"
 	"github.com/aoagents/agent-orchestrator/backend/internal/lifecycle"
 	"github.com/aoagents/agent-orchestrator/backend/internal/ports"
-	"github.com/aoagents/agent-orchestrator/backend/internal/project"
 	"github.com/aoagents/agent-orchestrator/backend/internal/storage/sqlite"
 )
 
@@ -37,7 +36,7 @@ func TestWiring_WriteFlowsToBroadcaster(t *testing.T) {
 	var got []cdc.Event
 	bcast.Subscribe(func(e cdc.Event) { mu.Lock(); got = append(got, e); mu.Unlock() })
 
-	if err := store.Upsert(ctx, project.Row{ID: "mer", Path: "/repo/mer"}); err != nil {
+	if err := store.UpsertProject(ctx, domain.ProjectRecord{ID: "mer", Path: "/repo/mer"}); err != nil {
 		t.Fatal(err)
 	}
 	rec, err := store.CreateSession(ctx, domain.SessionRecord{

backend/internal/domain/project.go

@@ -0,0 +1,13 @@
+package domain
+
+import "time"
+
+// ProjectRecord is the durable project registry row used by storage and services.
+type ProjectRecord struct {
+	ID            string
+	Path          string
+	RepoOriginURL string
+	DisplayName   string
+	RegisteredAt  time.Time
+	ArchivedAt    time.Time
+}

backend/internal/httpd/api.go

@@ -10,15 +10,15 @@ import (
 	"github.com/aoagents/agent-orchestrator/backend/internal/httpd/apispec"
 	"github.com/aoagents/agent-orchestrator/backend/internal/httpd/controllers"
 	"github.com/aoagents/agent-orchestrator/backend/internal/httpd/envelope"
-	"github.com/aoagents/agent-orchestrator/backend/internal/project"
+	projectsvc "github.com/aoagents/agent-orchestrator/backend/internal/service/project"
 )
 
 // APIDeps bundles every Manager the API layer's controllers depend on.
 // Controllers see only resource-level interfaces; they do not reach through to
 // lifecycle reducers, adapters, or storage. A nil dependency keeps its routes
 // registered but returns the OpenAPI-backed 501 response.
 type APIDeps struct {
-	Projects project.Manager
+	Projects projectsvc.Manager
 	Sessions controllers.SessionService
 }
 

backend/internal/httpd/apispec/apispec.go

@@ -27,7 +27,8 @@ var openapiYAML []byte
 // preserves the YAML shape verbatim so the JSON we emit on 501 responses
 // matches the on-disk source.
 type Spec struct {
-	doc map[string]any
+	doc     map[string]any
+	rawYAML []byte
 }
 
 var (
@@ -61,7 +62,12 @@ func New(yamlBytes []byte) (*Spec, error) {
 	if doc == nil {
 		return nil, fmt.Errorf("parse openapi: empty document")
 	}
-	return &Spec{doc: doc}, nil
+	return &Spec{doc: doc, rawYAML: yamlBytes}, nil
+}
+
+// YAML returns the raw YAML bytes this spec was built from.
+func (s *Spec) YAML() []byte {
+	return s.rawYAML
 }
 
 // Operation returns the spec slice for a single (method, path) pair, ready