feat: RDF 1.2 reifier migration + Prolog→SHACL + addListener→subscribeQuery + N+1 elimination

[HexaField]

Summary

This PR combines the full SPARQL 1.2 migration for Flux — originally split across feat/sparql-1.2 (#590, now closed) and feat/sparql-1.2-cleanup (#591). Together they deliver: all custom SPARQL queries migrated to RDF 1.2 reifier patterns, all Prolog replaced with SHACL APIs, all global addListener patterns replaced with targeted subscribeQuery, and all N+1 query patterns eliminated.

Companion: AD4M coasys/ad4m#803

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Part 1: Migrate Flux SPARQL Queries to RDF 1.2 Reifier Patterns

(Originally #590)

Migrates all custom SPARQL queries in Flux API packages from the old named-graph GRAPH ?g { s p o } pattern to direct default-graph triples with RDF 1.2 reifier patterns for link metadata.

Changes

packages/api/src/channel/index.ts

• allItems() — direct triple pattern, no GRAPH
• unprocessedItems() — 3 subqueries converted (all items, processed items, set-difference)
• totalItemCount() — direct pattern
• recentConversations() — reifier for timestamp
• pinnedConversations() — direct pattern

packages/api/src/conversation/index.ts

• stats() subgroups query — direct pattern
• topics() — direct pattern (5 GRAPH vars → direct triples)
• subgroupsData() main query — reifier for timestamp on has_child link
• subgroupsData() batch timestamp query — reifier for channel timestamp

packages/api/src/conversation-subgroup/index.ts

• stats() — direct pattern
• topics() — direct pattern
• itemsData() — reifier for both subgroup-item timestamp and type-link author, plus channel timestamp
• topicsWithRelevance() — direct pattern

app/src/utils/registerMobileNotifications.ts

• Mobile push notification trigger query — removed GRAPH wrapper

Other

• Added type-checking support in the CI pipeline
• Improved timeline subscription refresh for more responsive conversation updates
• Safer handling of missing channel data to prevent navigation/display errors
• Normalized community IDs to fix membership edge cases
• Improved mobile notification matching and AI task processing reliability
• More accurate timestamp selection for conversation ordering
• Expanded unit and integration tests for channels, conversations, and timeline subscriptions
• Integrated linting and type-checking gates into CI; updated ESLint config and ignore list

Pattern Migration

Before (named graphs):

GRAPH ?link1 { <parent> <ad4m://has_child> ?id . }
?link1 <ad4m://ontology/timestamp> ?timestamp .

After (RDF 1.2 reifiers):

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
<parent> <ad4m://has_child> ?id .
?_reifier rdf:reifies <<( <parent> <ad4m://has_child> ?id )>> .
?_reifier <ad4m://ontology/timestamp> ?timestamp .

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Part 2: Prolog → SHACL, addListener → subscribeQuery, N+1 Elimination

(Originally #591)

26 files changed, 514 insertions, 659 deletions (net −145 lines)

After this part, zero perspective.infer() calls, zero unfocused addListener patterns, and zero global link bus usage remain in Flux app/view source code.

Prolog → SPARQL Conversions

File	What changed
topic/index.ts	linkedConversations() / linkedSubgroups() → SPARQL
semantic-relationship/index.ts	All 5 methods → SPARQL
conversation/util.ts	findEmbeddingSRId() → SPARQL

addListener → Targeted subscribeQuery

File	What changed
flux-container.ts	Global listener → subscribeQuery with Channel SPARQL
CommentSection.tsx	Global listener → subscribeQuery on source
CommunityGraph.tsx	Global listener → subscribeQuery on source/target (was leaking, now properly cleaned up)
useAssociations.tsx	Global listener → subscribeQuery with proper dispose
TimelineColumn.tsx	Global listener → subscribeQuery
useCommunityService.ts	Participant tracking → subscribeQuery on CHANNEL predicate
cache.tsx	Deleted unused subscribeToPerspective / unsubscribeToPerspective (zero callers, contained addListener)

N+1 Query Elimination

File	What changed
useCommunityService.ts	Nested Promise.all → two-phase batch (link queries then conversation lookups)
CommentSection.tsx	N × Message.get() → Message.findAll({ parent })
PollCard.tsx	Per-answer Vote.findAll → useLiveQuery(Answer, { include: { votes: true } })

kanban-view Migration

File	What changed
Board.tsx	.infer() → listRegisteredClasses() + getNamedOptions() + addNamedOption() + ensureSDNASubjectClass(Task). Task creation uses initialValues.
Entry.tsx	.infer(property_named_option) → getNamedOptions()
TaskModel.ts	New — TypeScript @Model class with @Property({ options: [...] }) for status enum
Task.pl	Deleted (22 lines of Prolog SDNA)

table-view Migration

File	What changed
TableView.tsx	.infer(subject_class) → listRegisteredClasses()
Table.tsx	.infer(property_named_option) → getNamedOptions(). Updates use getClassShape() for predicate resolution + direct link manipulation.
Header.tsx	.infer() → getInstanceClasses() + getSubjectData(). Updates via getClassShape() + link add/remove.
Entry.tsx	Same as Header
History.tsx	Same as Header (read-only)
NewClass.tsx	generateSDNA() (raw Prolog) → buildSHACLShape() + addShacl(). Removed makeRandomPrologAtom().

Global Link Bus Removal

File	What changed
MainView.vue	Removed gotNewMessage, onLinkAdded, and associated addLink bus emissions
usePerspectives.ts	Deleted addListeners(), onLinkAdded(), onLinkRemoved(), and link callback arrays — the global link event bus is gone

Other

• createCommunity.ts: .timestamp → .createdAt (deprecated alias removed in companion PR)

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Depends On

AD4M coasys/ad4m#803 — provides Oxigraph 0.5.7 + RDF 1.2 reifiers, Rust model query engine, getNamedOptions(), addNamedOption(), listRegisteredClasses(), getClassShape(), getInstanceClasses(), getSubjectData(), SHACLShape, @Property({ options }), perspectiveModelSubscribe

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Expected Performance Impact

• Link listener overhead: Near-zero — global addListener callbacks (fired on every link change across every perspective) replaced with targeted subscribeQuery that only fires when matching predicates change. In a community with 10+ channels, this eliminates ~90% of spurious JS callback invocations.
• N+1 queries: Batch operations (findAll with include) replace per-item .get() calls, reducing round-trips from N+1 to 1-2 per list render.
• kanban/table views: Prolog infer() calls (which loaded and evaluated the entire SDNA program) replaced with direct SHACL API lookups.
• Vue reactivity: Removing the global link bus prevents unnecessary re-renders in components that don't care about the changed links.

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