fix(markedup): preserve semantic relationships after module bump

go.mod

@@ -3,7 +3,7 @@ module github.com/Clarit-AI/Plexium
 go 1.25.1
 
 require (
-	github.com/Clarit-AI/markedup v0.0.0-20260418185353-12e3cc5f0d89
+	github.com/Clarit-AI/markedup v0.0.0-20260419063450-0c5745b5a986
 	github.com/bmatcuk/doublestar/v2 v2.0.4
 	github.com/gobwas/glob v0.2.3
 	github.com/pelletier/go-toml/v2 v2.1.0
@@ -33,6 +33,7 @@ require (
 	golang.org/x/exp v0.0.0-20230905200255-921286631fa9 // indirect
 	golang.org/x/sync v0.20.0 // indirect
 	golang.org/x/sys v0.38.0 // indirect
+	golang.org/x/term v0.3.0 // indirect
 	golang.org/x/text v0.14.0 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 )

go.sum

@@ -1,5 +1,5 @@
-github.com/Clarit-AI/markedup v0.0.0-20260418185353-12e3cc5f0d89 h1:7DxgiIXe17JLwfjaE+YnAmMzzTqneVvjMCn7baLY4G4=
-github.com/Clarit-AI/markedup v0.0.0-20260418185353-12e3cc5f0d89/go.mod h1:IMDGULtUy68kQ1dKlDgT7gD9lD7KJZ0dDRDPqf79x9s=
+github.com/Clarit-AI/markedup v0.0.0-20260419063450-0c5745b5a986 h1:7wQfT3hNTXKTcAFrJnQMJmOTzxAJ6/HQKUiDDpfbS9o=
+github.com/Clarit-AI/markedup v0.0.0-20260419063450-0c5745b5a986/go.mod h1:Dpgx+f+jzufgRjrHkujDruoKOJOh0H7EtHcyRpliXWQ=
 github.com/bmatcuk/doublestar/v2 v2.0.4 h1:6I6oUiT/sU27eE2OFcWqBhL1SwjyvQuOssxT4a1yidI=
 github.com/bmatcuk/doublestar/v2 v2.0.4/go.mod h1:QMmcs3H2AUQICWhfzLXz+IYln8lRQmTZRptLie8RgRw=
 github.com/cpuguy83/go-md2man/v2 v2.0.4/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o=
@@ -72,6 +72,8 @@ golang.org/x/sync v0.20.0 h1:e0PTpb7pjO8GAtTs2dQ6jYa5BWYlMuX047Dco/pItO4=
 golang.org/x/sync v0.20.0/go.mod h1:9xrNwdLfx4jkKbNva9FpL6vEN7evnE43NNNJQ2LF3+0=
 golang.org/x/sys v0.38.0 h1:3yZWxaJjBmCWXqhN1qh02AkOnCQ1poK6oF+a7xWL6Gc=
 golang.org/x/sys v0.38.0/go.mod h1:OgkHotnGiDImocRcuBABYBEXf8A9a87e/uXjp9XT3ks=
+golang.org/x/term v0.3.0 h1:qoo4akIqOcDME5bhc/NgxUdovd6BSS2uMsVjB56q1xI=
+golang.org/x/term v0.3.0/go.mod h1:q750SLmJuPmVoN1blW3UFBPREJfb1KmY3vwxfr+nFDA=
 golang.org/x/text v0.14.0 h1:ScX5w1eTa3QqT8oi6+ziP7dTV1S2+ALU0bI+0zXKWiQ=
 golang.org/x/text v0.14.0/go.mod h1:18ZOQIKpY8NJVqYksKHtTdi31H5itFRjB5/qKTNYzSU=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=

internal/convert/ingest.go

@@ -257,7 +257,7 @@ func (ing *Ingestor) buildModulePage(readme ReadmeDoc) string {
 	b.WriteString(fmt.Sprintf("last-updated: %s\n", now))
 	b.WriteString("updated-by: plexium-convert\n")
 	b.WriteString(fmt.Sprintf("source-files: [\"%s\"]\n", readme.Path))
-	b.WriteString("confidence: high\n")
+	b.WriteString("confidence: 0.9\n")
 	b.WriteString("review-status: unreviewed\n")
 	b.WriteString("---\n\n")
 	b.WriteString(readme.Content)
@@ -275,7 +275,7 @@ func (ing *Ingestor) buildModuleStubPage(name string, files []string) string {
 	b.WriteString("ownership: managed\n")
 	b.WriteString(fmt.Sprintf("last-updated: %s\n", now))
 	b.WriteString("updated-by: plexium-convert\n")
-	b.WriteString("confidence: medium\n")
+	b.WriteString("confidence: 0.5\n")
 	b.WriteString("review-status: unreviewed\n")
 	b.WriteString("---\n\n")
 	b.WriteString(fmt.Sprintf("# %s\n\n", title))
@@ -315,7 +315,7 @@ func (ing *Ingestor) buildGuidePage(title, content string) string {
 	b.WriteString("ownership: managed\n")
 	b.WriteString(fmt.Sprintf("last-updated: %s\n", now))
 	b.WriteString("updated-by: plexium-convert\n")
-	b.WriteString("confidence: medium\n")
+	b.WriteString("confidence: 0.5\n")
 	b.WriteString("review-status: unreviewed\n")
 	b.WriteString("---\n\n")
 	b.WriteString(content)

internal/convert/lint.go

@@ -131,7 +131,7 @@ func (cl *ConvertLinter) createStub(moduleName string) PageData {
 	b.WriteString("---\n")
 	b.WriteString(fmt.Sprintf("title: %q\n", title))
 	b.WriteString("ownership: managed\n")
-	b.WriteString("confidence: low\n")
+	b.WriteString("confidence: 0.1\n")
 	b.WriteString("review-status: unreviewed\n")
 	b.WriteString("---\n\n")
 	b.WriteString(fmt.Sprintf("# %s\n\n", title))

internal/manifest/manifest.go

@@ -43,13 +43,14 @@ type PageEntry struct {
 	// "I have zero confidence" signal is semantically equivalent to
 	// "unset" for current consumers — if we ever need to distinguish
 	// the two cases we should switch this to *float64 at that point.
-	EntityType    string            `json:"entityType,omitempty"`
-	Entities      []EntityRef       `json:"entities,omitempty"`
-	Relationships []RelationshipRef `json:"relationships,omitempty"`
-	Confidence    float64           `json:"confidence,omitempty"`
-	SemanticHints []string          `json:"semanticHints,omitempty"`
-	LastEnriched  string            `json:"lastEnriched,omitempty"`
-	EnrichedBy    string            `json:"enrichedBy,omitempty"`
+	EntityType            string            `json:"entityType,omitempty"`
+	Entities              []EntityRef       `json:"entities,omitempty"`
+	Relationships         []RelationshipRef `json:"relationships,omitempty"`
+	SemanticRelationships []RelationshipRef `json:"semanticRelationships,omitempty"`
+	Confidence            float64           `json:"confidence,omitempty"`
+	SemanticHints         []string          `json:"semanticHints,omitempty"`
+	LastEnriched          string            `json:"lastEnriched,omitempty"`
+	EnrichedBy            string            `json:"enrichedBy,omitempty"`
 }
 
 // EntityRef is a reference to a named entity on a page. It mirrors the
@@ -182,13 +183,14 @@ func NewEmptyManifest() *Manifest {
 // GraphMetadata bundles the knowledge-graph fields set by an enrichment
 // plugin. It's accepted by ApplyGraphMetadata to update a page in-place.
 type GraphMetadata struct {
-	EntityType    string
-	Entities      []EntityRef
-	Relationships []RelationshipRef
-	Confidence    float64
-	SemanticHints []string
-	LastEnriched  string
-	EnrichedBy    string
+	EntityType            string
+	Entities              []EntityRef
+	Relationships         []RelationshipRef
+	SemanticRelationships []RelationshipRef
+	Confidence            float64
+	SemanticHints         []string
+	LastEnriched          string
+	EnrichedBy            string
 }
 
 // ApplyGraphMetadata overwrites the v2 graph fields on the page entry with
@@ -204,6 +206,7 @@ func (m *Manifest) ApplyGraphMetadata(wikiPath string, g GraphMetadata) bool {
 		m.Pages[i].EntityType = g.EntityType
 		m.Pages[i].Entities = g.Entities
 		m.Pages[i].Relationships = g.Relationships
+		m.Pages[i].SemanticRelationships = g.SemanticRelationships
 		m.Pages[i].Confidence = g.Confidence
 		m.Pages[i].SemanticHints = g.SemanticHints
 		m.Pages[i].LastEnriched = g.LastEnriched
@@ -222,6 +225,7 @@ func hasGraphFields(g GraphMetadata) bool {
 	return g.EntityType != "" ||
 		len(g.Entities) > 0 ||
 		len(g.Relationships) > 0 ||
+		len(g.SemanticRelationships) > 0 ||
 		g.Confidence != 0 ||
 		len(g.SemanticHints) > 0 ||
 		g.LastEnriched != "" ||
@@ -243,13 +247,14 @@ func (m *Manifest) GraphMetadataForPage(wikiPath string) (GraphMetadata, bool) {
 		}
 		p := m.Pages[i]
 		return GraphMetadata{
-			EntityType:    p.EntityType,
-			Entities:      p.Entities,
-			Relationships: p.Relationships,
-			Confidence:    p.Confidence,
-			SemanticHints: p.SemanticHints,
-			LastEnriched:  p.LastEnriched,
-			EnrichedBy:    p.EnrichedBy,
+			EntityType:            p.EntityType,
+			Entities:              p.Entities,
+			Relationships:         p.Relationships,
+			SemanticRelationships: p.SemanticRelationships,
+			Confidence:            p.Confidence,
+			SemanticHints:         p.SemanticHints,
+			LastEnriched:          p.LastEnriched,
+			EnrichedBy:            p.EnrichedBy,
 		}, true
 	}
 	return GraphMetadata{}, false
@@ -290,6 +295,14 @@ func GraphMetadataSemanticEqual(a, b GraphMetadata) bool {
 			return false
 		}
 	}
+	if len(a.SemanticRelationships) != len(b.SemanticRelationships) {
+		return false
+	}
+	for i := range a.SemanticRelationships {
+		if a.SemanticRelationships[i] != b.SemanticRelationships[i] {
+			return false
+		}
+	}
 	if len(a.SemanticHints) != len(b.SemanticHints) {
 		return false
 	}

internal/plugins/markedup/config.go

@@ -18,6 +18,7 @@ package markedup
 
 import (
 	"fmt"
+	"strings"
 	"time"
 )
 
@@ -144,9 +145,9 @@ func DefaultConfig() Config {
 // root of the plugins.markedup block. Anything else is a config error.
 var allowedTopLevelKeys = map[string]struct{}{
 	"enabled":                  {},
-	"autoEnrich":               {},
-	"modelEnrich":              {},
-	"writeEnrichedFrontmatter": {},
+	"autoenrich":               {},
+	"modelenrich":              {},
+	"writeenrichedfrontmatter": {},
 	"embeddings":               {},
 	"reranking":                {},
 	"daemon":                   {},
@@ -155,7 +156,7 @@ var allowedTopLevelKeys = map[string]struct{}{
 // allowedDaemonKeys constrains the nested daemon block (see allowed*Keys
 // for the rationale).
 var allowedDaemonKeys = map[string]struct{}{
-	"refreshInterval": {},
+	"refreshinterval": {},
 }
 
 // allowedEmbeddingsKeys and allowedRerankingKeys constrain the nested
@@ -166,7 +167,7 @@ var allowedEmbeddingsKeys = map[string]struct{}{
 	"provider":  {},
 	"model":     {},
 	"endpoint":  {},
-	"apiKeyEnv": {},
+	"apikeyenv": {},
 	"dims":      {},
 }
 
@@ -175,7 +176,7 @@ var allowedRerankingKeys = map[string]struct{}{
 	"provider":  {},
 	"model":     {},
 	"endpoint":  {},
-	"apiKeyEnv": {},
+	"apikeyenv": {},
 }
 
 // ParseConfig reads the plugins.markedup block from the raw map form used
@@ -191,6 +192,8 @@ var allowedRerankingKeys = map[string]struct{}{
 //   - An unknown key, a malformed nested block, or an invalid value
 //     (e.g. non-positive embeddings.dims) returns an error.
 func ParseConfig(raw map[string]any) (Config, error) {
+	normalizeKeys(raw)
+
 	cfg := DefaultConfig()
 	cfg.Enabled = false // strict: only an explicit `enabled: true` turns it on
 	if len(raw) == 0 {
@@ -206,19 +209,19 @@ func ParseConfig(raw map[string]any) (Config, error) {
 	} else if _, present := raw["enabled"]; present {
 		return Config{}, fmt.Errorf("markedup.enabled must be a boolean")
 	}
-	if v, ok := raw["autoEnrich"].(bool); ok {
+	if v, ok := raw["autoenrich"].(bool); ok {
 		cfg.AutoEnrich = v
-	} else if _, present := raw["autoEnrich"]; present {
+	} else if _, present := raw["autoenrich"]; present {
 		return Config{}, fmt.Errorf("markedup.autoEnrich must be a boolean")
 	}
-	if v, ok := raw["modelEnrich"].(bool); ok {
+	if v, ok := raw["modelenrich"].(bool); ok {
 		cfg.ModelEnrich = v
-	} else if _, present := raw["modelEnrich"]; present {
+	} else if _, present := raw["modelenrich"]; present {
 		return Config{}, fmt.Errorf("markedup.modelEnrich must be a boolean")
 	}
-	if v, ok := raw["writeEnrichedFrontmatter"].(bool); ok {
+	if v, ok := raw["writeenrichedfrontmatter"].(bool); ok {
 		cfg.WriteEnrichedFrontmatter = v
-	} else if _, present := raw["writeEnrichedFrontmatter"]; present {
+	} else if _, present := raw["writeenrichedfrontmatter"]; present {
 		return Config{}, fmt.Errorf("markedup.writeEnrichedFrontmatter must be a boolean")
 	}
 
@@ -244,7 +247,7 @@ func ParseConfig(raw map[string]any) (Config, error) {
 		if v, ok := emb["endpoint"].(string); ok {
 			cfg.Embeddings.Endpoint = v
 		}
-		if v, ok := emb["apiKeyEnv"].(string); ok {
+		if v, ok := emb["apikeyenv"].(string); ok {
 			cfg.Embeddings.APIKeyEnv = v
 		}
 		if dimsRaw, p := emb["dims"]; p {
@@ -278,7 +281,7 @@ func ParseConfig(raw map[string]any) (Config, error) {
 		if v, ok := rr["endpoint"].(string); ok {
 			cfg.Reranking.Endpoint = v
 		}
-		if v, ok := rr["apiKeyEnv"].(string); ok {
+		if v, ok := rr["apikeyenv"].(string); ok {
 			cfg.Reranking.APIKeyEnv = v
 		}
 	}
@@ -291,9 +294,9 @@ func ParseConfig(raw map[string]any) (Config, error) {
 		if err := rejectUnknownKeys("markedup.daemon", dm, allowedDaemonKeys); err != nil {
 			return Config{}, err
 		}
-		if v, ok := dm["refreshInterval"].(string); ok {
+		if v, ok := dm["refreshinterval"].(string); ok {
 			cfg.Daemon.RefreshInterval = v
-		} else if _, p := dm["refreshInterval"]; p {
+		} else if _, p := dm["refreshinterval"]; p {
 			return Config{}, fmt.Errorf("markedup.daemon.refreshInterval must be a string (e.g. \"24h\")")
 		}
 	}
@@ -304,11 +307,30 @@ func ParseConfig(raw map[string]any) (Config, error) {
 	return cfg, nil
 }
 
+// normalizeKeys recursively lowercases all string keys in the map.
+// Viper lowercases YAML keys when decoding to map[string]any, but
+// tests and other callers may pass camelCase keys directly. This
+// ensures lookups in ParseConfig always use lowercase keys.
+func normalizeKeys(m map[string]any) {
+	for k, v := range m {
+		lower := strings.ToLower(k)
+		if lower != k {
+			delete(m, k)
+			m[lower] = v
+		}
+		if nested, ok := v.(map[string]any); ok {
+			normalizeKeys(nested)
+		}
+	}
+}
+
 // rejectUnknownKeys returns a config error if got contains any key that
 // isn't in allowed. scope is prepended to the error message for context.
+// Keys are compared case-insensitively because Viper lowercases all map
+// keys on unmarshal.
 func rejectUnknownKeys(scope string, got map[string]any, allowed map[string]struct{}) error {
 	for k := range got {
-		if _, ok := allowed[k]; !ok {
+		if _, ok := allowed[strings.ToLower(k)]; !ok {
 			return fmt.Errorf("%s: unknown key %q", scope, k)
 		}
 	}

internal/plugins/markedup/enricher.go

@@ -387,16 +387,26 @@ func toGraphMetadata(fm schema.GraphFrontmatter, timestamp string) manifest.Grap
 		})
 	}
 
+	semanticRels := make([]manifest.RelationshipRef, 0, len(fm.SemanticRelationships))
+	for _, r := range fm.SemanticRelationships {
+		semanticRels = append(semanticRels, manifest.RelationshipRef{
+			Target:   r.Target,
+			Type:     r.Type,
+			Strength: r.Strength,
+		})
+	}
+
 	hints := make([]string, len(fm.SemanticHints))
 	copy(hints, fm.SemanticHints)
 
 	return manifest.GraphMetadata{
-		EntityType:    fm.EntityType,
-		Entities:      entities,
-		Relationships: rels,
-		Confidence:    fm.Confidence,
-		SemanticHints: hints,
-		LastEnriched:  timestamp,
-		EnrichedBy:    EnricherVersion,
+		EntityType:            fm.EntityType,
+		Entities:              entities,
+		Relationships:         rels,
+		SemanticRelationships: semanticRels,
+		Confidence:            fm.Confidence,
+		SemanticHints:         hints,
+		LastEnriched:          timestamp,
+		EnrichedBy:            EnricherVersion,
 	}
 }

internal/plugins/markedup/enricher_modelenrich_test.go

@@ -35,7 +35,7 @@ func (f *fakeLLM) ExtractGraph(ctx context.Context, body string) (*enrich.ModelR
 // what Tier 1 produced.
 func TestEnricherPlugin_ModelEnrichMergesLLMResult(t *testing.T) {
 	repoRoot, wikiRoot := setupWikiFixture(t, map[string]string{
-		"a.md": "# A\n\nThis page is about authentication.\n",
+		"a.md": "# A\n\nRelates to [[b]].\nThis page is about authentication.\n",
 	})
 
 	llm := &fakeLLM{
@@ -89,15 +89,25 @@ func TestEnricherPlugin_ModelEnrichMergesLLMResult(t *testing.T) {
 	if !foundOAuth || !foundJWT {
 		t.Errorf("expected OAuth2 and JWT entities from LLM; got %+v", entry.Entities)
 	}
-	// LLM-extracted relationship should appear too.
-	foundRel := false
+	// Tier 1 wikilink should be in entry.Relationships.
+	foundB := false
 	for _, r := range entry.Relationships {
+		if r.Target == "b" {
+			foundB = true
+		}
+	}
+	if !foundB {
+		t.Errorf("expected Tier 1 wikilink to survive in Relationships; got %+v", entry.Relationships)
+	}
+	// Tier 2 NER edge should be in SemanticRelationships.
+	foundAuthServer := false
+	for _, r := range entry.SemanticRelationships {
 		if r.Target == "auth-server" && r.Type == "depends-on" {
-			foundRel = true
+			foundAuthServer = true
 		}
 	}
-	if !foundRel {
-		t.Errorf("expected auth-server relationship from LLM; got %+v", entry.Relationships)
+	if !foundAuthServer {
+		t.Errorf("expected Tier 2 NER edge to appear in SemanticRelationships; got %+v", entry.SemanticRelationships)
 	}
 	if entry.EnrichedBy != EnricherVersion {
 		t.Errorf("expected EnrichedBy=%q, got %q", EnricherVersion, entry.EnrichedBy)