fix(ci): resolve CI failures, skip warm-start ANALYZE, add init timing logs

kmp/build.gradle.kts

@@ -93,8 +93,6 @@ kotlin {
                 // Okio — cross-platform file I/O for asset management
                 implementation("com.squareup.okio:okio:3.17.0")
 
-                // ktoml — TOML parsing for .stele-sections manifest
-                implementation("com.akuleshov7:ktoml-core:0.7.1")
             }
         }
 
@@ -103,6 +101,9 @@ kotlin {
             dependencies {
                 // OpenTelemetry API — JVM/Android only (not available for wasmJs)
                 implementation("io.opentelemetry:opentelemetry-api:1.43.0")
+                // ktoml — TOML parsing for .stele-sections manifest (excluded from wasmJs:
+                // ktoml generates WASM bytecode that fails wasm-opt validation)
+                implementation("com.akuleshov7:ktoml-core:0.7.1")
             }
         }
 
@@ -313,6 +314,10 @@ kotlin {
 
                 // Kable — Kotlin coroutine BLE for iOS/Apple targets (CoreBluetooth wrapper)
                 implementation("com.juul.kable:core:0.32.0")
+
+                // ktoml — TOML parsing for .stele-sections manifest (actual impl for iOS;
+                // excluded from commonMain to avoid invalid WASM bytecode on wasmJs target)
+                implementation("com.akuleshov7:ktoml-core:0.7.1")
             }
         }
 

kmp/src/androidMain/kotlin/BUILD.bazel

@@ -97,6 +97,9 @@ kt_android_library(
         "@maven//:io_opentelemetry_opentelemetry_sdk",
         "@maven//:io_opentelemetry_opentelemetry_exporter_logging",
 
+        # ktoml — TOML parsing for .stele-sections manifest (from commonMain)
+        "@maven//:com_akuleshov7_ktoml_core_jvm",
+
         # Ksoup (from commonMain)
         "@maven//:com_fleeksoft_ksoup_ksoup_jvm",
 

kmp/src/commonMain/kotlin/dev/stapler/stelekit/db/GraphManager.kt

@@ -378,7 +378,11 @@ class GraphManager(
         // never hangs permanently.
         graphScope.launch(PlatformDispatcher.IO) {
             try {
+                val t0 = kotlin.time.Clock.System.now().toEpochMilliseconds()
+                fun elapsed() = kotlin.time.Clock.System.now().toEpochMilliseconds() - t0
+
                 preFlightJob?.await()
+                logger.info("init[${elapsed()}ms]: preFlightJob done")
 
                 val dbUrl = driverFactory.getDatabaseUrl(id)
                 val factory = dev.stapler.stelekit.repository.RepositoryFactoryImpl(driverFactory, dbUrl, graphId = id)
@@ -396,6 +400,7 @@ class GraphManager(
                     appVersion = deviceInfo?.appVersion ?: "unknown",
                     platform = deviceInfo?.platform ?: "unknown",
                 )
+                logger.info("init[${elapsed()}ms]: createRepositorySet done")
                 currentFactory = factory
                 _activeRepositorySet.value = repoSet
 
@@ -404,6 +409,7 @@ class GraphManager(
                     if (writeActor != null) {
                         val db = factory.steleDatabase()
                         UuidMigration(writeActor).runIfNeeded(db)
+                        logger.info("init[${elapsed()}ms]: UuidMigration done")
                         try {
                             MigrationRunner(
                                 registry = MigrationRegistry,
@@ -417,6 +423,7 @@ class GraphManager(
                         } catch (e: MigrationTamperedError) {
                             logger.error("MigrationRunner: tampered migration detected for graph $id", e)
                         }
+                        logger.info("init[${elapsed()}ms]: content migrations done")
                     }
                 }
             } catch (e: CancellationException) {

kmp/src/commonMain/kotlin/dev/stapler/stelekit/db/MigrationRunner.kt

@@ -828,12 +828,24 @@ object MigrationRunner {
         // driver throws when execSQL is called for result-returning statements. It is set in
         // ANDROID_PRAGMAS via the rawQuery path (DriverFactory.android.kt) and in
         // buildMainDbConnectionProps() for JVM so every pool connection inherits it.
-        driver.execute(null, "ANALYZE blocks", 0).await()
-        driver.execute(null, "ANALYZE pages", 0).await()
-        // PRAGMA optimize is still useful for other tables we don't explicitly analyze above.
+        // ponytail: only ANALYZE when stats are absent; PRAGMA optimize handles stale stats
+        if (!hasStats(driver, "blocks")) driver.execute(null, "ANALYZE blocks", 0).await()
+        if (!hasStats(driver, "pages")) driver.execute(null, "ANALYZE pages", 0).await()
         driver.execute(null, "PRAGMA optimize", 0).await()
     }
 
+    // Returns false if sqlite_stat1 doesn't exist yet or has no row for [table].
+    private suspend fun hasStats(driver: SqlDriver, table: String): Boolean = try {
+        driver.executeQuery(
+            identifier = null,
+            sql = "SELECT count(*) FROM sqlite_stat1 WHERE tbl = '$table'",
+            mapper = { cursor -> cursor.next(); QueryResult.Value((cursor.getLong(0) ?: 0L) > 0L) },
+            parameters = 0
+        ).await()
+    } catch (_: Exception) {
+        false
+    }
+
     internal suspend fun applyAll(driver: SqlDriver, migrations: List<Migration>) {
         // Bootstrap the tracking table — must succeed before anything else.
         driver.execute(

kmp/src/commonMain/kotlin/dev/stapler/stelekit/sections/SectionManifestParser.kt

@@ -3,14 +3,9 @@ package dev.stapler.stelekit.sections
 import arrow.core.Either
 import arrow.core.left
 import arrow.core.right
-import com.akuleshov7.ktoml.Toml
-import com.akuleshov7.ktoml.TomlInputConfig
 import dev.stapler.stelekit.error.DomainError
 import dev.stapler.stelekit.platform.FileSystem
 import kotlinx.coroutines.CancellationException
-import kotlinx.serialization.serializer
-
-internal val sectionToml = Toml(inputConfig = TomlInputConfig(ignoreUnknownNames = true))
 
 class SectionManifestParser(private val fileSystem: FileSystem) {
 
@@ -23,11 +18,16 @@ class SectionManifestParser(private val fileSystem: FileSystem) {
             ?: return DomainError.FileSystemError.ReadFailed(path, "could not read manifest").left()
 
         return try {
-            sectionToml.decodeFromString(serializer<SectionManifest>(), content).right()
+            (decodeSectionManifestToml(content) ?: SectionManifest()).right()
         } catch (e: CancellationException) {
             throw e
         } catch (e: Exception) {
             DomainError.ParseError.InvalidSyntax("${SectionManifest.FILENAME}: ${e.message ?: "invalid TOML"}").left()
         }
     }
 }
+
+// ktoml doesn't support Kotlin/Wasm — platform actuals provide real parsing/writing on JVM/iOS,
+// stubs on WASM (parser falls back to empty SectionManifest; writer catches the exception).
+internal expect fun decodeSectionManifestToml(content: String): SectionManifest?
+internal expect fun encodeSectionManifestToml(manifest: SectionManifest): String

kmp/src/commonMain/kotlin/dev/stapler/stelekit/sections/SectionManifestWriter.kt

@@ -6,15 +6,13 @@ import arrow.core.right
 import dev.stapler.stelekit.error.DomainError
 import dev.stapler.stelekit.platform.FileSystem
 import kotlinx.coroutines.CancellationException
-import kotlinx.serialization.serializer
-
 class SectionManifestWriter(private val fileSystem: FileSystem) {
 
     fun write(graphPath: String, manifest: SectionManifest): Either<DomainError, Unit> {
         val base = if (graphPath.endsWith("/")) graphPath else "$graphPath/"
         val path = "$base${SectionManifest.FILENAME}"
         return try {
-            val content = sectionToml.encodeToString(serializer<SectionManifest>(), manifest)
+            val content = encodeSectionManifestToml(manifest)
             if (fileSystem.writeFile(path, content)) Unit.right()
             else DomainError.FileSystemError.WriteFailed(path, "write returned false").left()
         } catch (e: CancellationException) {

kmp/src/commonMain/kotlin/dev/stapler/stelekit/ui/components/SectionBadge.kt

@@ -28,8 +28,8 @@ import dev.stapler.stelekit.sections.SectionDefinition
 @Composable
 fun SectionBadge(
     section: SectionDefinition,
-    onClick: (() -> Unit)? = null,
     modifier: Modifier = Modifier,
+    onClick: (() -> Unit)? = null,
 ) {
     val dotColor = remember(section.color) {
         section.color?.let {

kmp/src/commonMain/kotlin/dev/stapler/stelekit/ui/components/settings/SettingsDialog.kt

@@ -214,15 +214,18 @@ fun SettingsDialog(
                                         onLibsqlDriverToggle = onLibsqlDriverToggle,
                                     )
                                 }
-                                SettingsCategory.SECTIONS -> if (sectionManifest != null &&
-                                    onCreateSection != null && onRenameSection != null && onDeleteSection != null
-                                ) {
-                                    SectionsSettings(
-                                        manifest = sectionManifest,
-                                        onCreateSection = onCreateSection,
-                                        onRenameSection = onRenameSection,
-                                        onDeleteSection = onDeleteSection,
-                                    )
+                                SettingsCategory.SECTIONS -> {
+                                    val canShowSections = sectionManifest != null &&
+                                        onCreateSection != null && onRenameSection != null &&
+                                        onDeleteSection != null
+                                    if (canShowSections) {
+                                        SectionsSettings(
+                                            manifest = sectionManifest!!,
+                                            onCreateSection = onCreateSection!!,
+                                            onRenameSection = onRenameSection!!,
+                                            onDeleteSection = onDeleteSection!!,
+                                        )
+                                    }
                                 }
                                 SettingsCategory.DEVICE_SUBSCRIPTIONS -> if (sectionManifest != null &&
                                     onToggleSectionState != null

kmp/src/commonMain/kotlin/dev/stapler/stelekit/ui/onboarding/DeviceSetupWizard.kt

@@ -108,16 +108,18 @@ private fun ModeSelectionContent(
     onPersonalMode: () -> Unit,
     onCustomMode: () -> Unit,
 ) {
-    Text("How will you use SteleKit on this device?", style = MaterialTheme.typography.bodyMedium)
-    Spacer(modifier = Modifier.height(8.dp))
-    OutlinedButton(onClick = onWorkMode, modifier = Modifier.fillMaxWidth()) {
-        Text("Work device — primary section only")
-    }
-    OutlinedButton(onClick = onPersonalMode, modifier = Modifier.fillMaxWidth()) {
-        Text("Personal device — all sections active")
-    }
-    OutlinedButton(onClick = onCustomMode, modifier = Modifier.fillMaxWidth()) {
-        Text("Custom")
+    Column {
+        Text("How will you use SteleKit on this device?", style = MaterialTheme.typography.bodyMedium)
+        Spacer(modifier = Modifier.height(8.dp))
+        OutlinedButton(onClick = onWorkMode, modifier = Modifier.fillMaxWidth()) {
+            Text("Work device — primary section only")
+        }
+        OutlinedButton(onClick = onPersonalMode, modifier = Modifier.fillMaxWidth()) {
+            Text("Personal device — all sections active")
+        }
+        OutlinedButton(onClick = onCustomMode, modifier = Modifier.fillMaxWidth()) {
+            Text("Custom")
+        }
     }
 }
 
@@ -150,39 +152,41 @@ private fun CustomModeContent(
     customDefaultSection: String,
     onDefaultChange: (String) -> Unit,
 ) {
-    Text("Section access:", style = MaterialTheme.typography.bodyMedium)
-    sections.forEach { section ->
-        val state = customStates[section.id] ?: SectionState.ACTIVE
-        Row(
-            modifier = Modifier.fillMaxWidth().padding(vertical = 4.dp),
-            verticalAlignment = Alignment.CenterVertically,
-        ) {
-            Text(section.displayName, modifier = Modifier.weight(1f))
-            TextButton(onClick = {
-                val next = when (state) {
-                    SectionState.ACTIVE -> SectionState.HIDDEN
-                    SectionState.HIDDEN -> SectionState.REMOVED
-                    SectionState.REMOVED -> SectionState.ACTIVE
+    Column {
+        Text("Section access:", style = MaterialTheme.typography.bodyMedium)
+        sections.forEach { section ->
+            val state = customStates[section.id] ?: SectionState.ACTIVE
+            Row(
+                modifier = Modifier.fillMaxWidth().padding(vertical = 4.dp),
+                verticalAlignment = Alignment.CenterVertically,
+            ) {
+                Text(section.displayName, modifier = Modifier.weight(1f))
+                TextButton(onClick = {
+                    val next = when (state) {
+                        SectionState.ACTIVE -> SectionState.HIDDEN
+                        SectionState.HIDDEN -> SectionState.REMOVED
+                        SectionState.REMOVED -> SectionState.ACTIVE
+                    }
+                    onStateChange(section.id, next)
+                }) {
+                    Text(state.name.lowercase().replaceFirstChar { it.uppercase() })
                 }
-                onStateChange(section.id, next)
-            }) {
-                Text(state.name.lowercase().replaceFirstChar { it.uppercase() })
             }
         }
-    }
-    Spacer(modifier = Modifier.height(8.dp))
-    Text("Default section (for new pages):", style = MaterialTheme.typography.bodyMedium)
-    Row(verticalAlignment = Alignment.CenterVertically) {
-        RadioButton(selected = customDefaultSection.isEmpty(), onClick = { onDefaultChange("") })
-        Text("Global", style = MaterialTheme.typography.bodyLarge)
-    }
-    sections.forEach { section ->
+        Spacer(modifier = Modifier.height(8.dp))
+        Text("Default section (for new pages):", style = MaterialTheme.typography.bodyMedium)
         Row(verticalAlignment = Alignment.CenterVertically) {
-            RadioButton(
-                selected = customDefaultSection == section.id,
-                onClick = { onDefaultChange(section.id) },
-            )
-            Text(section.displayName, style = MaterialTheme.typography.bodyLarge)
+            RadioButton(selected = customDefaultSection.isEmpty(), onClick = { onDefaultChange("") })
+            Text("Global", style = MaterialTheme.typography.bodyLarge)
+        }
+        sections.forEach { section ->
+            Row(verticalAlignment = Alignment.CenterVertically) {
+                RadioButton(
+                    selected = customDefaultSection == section.id,
+                    onClick = { onDefaultChange(section.id) },
+                )
+                Text(section.displayName, style = MaterialTheme.typography.bodyLarge)
+            }
         }
     }
 }

kmp/src/generated/sqldelight/dev/stapler/stelekit/db/SteleDatabaseQueries.kt

@@ -991,7 +991,11 @@ public class SteleDatabaseQueries(
     )
   }
 
-  public fun selectUnloadedPagesBySection(section_id: Collection<String>, value_: Long, value__: Long): Query<Pages> = selectUnloadedPagesBySection(section_id, value_, value__, ::Pages)
+  public fun selectUnloadedPagesBySection(
+    section_id: Collection<String>,
+    value_: Long,
+    value__: Long,
+  ): Query<Pages> = selectUnloadedPagesBySection(section_id, value_, value__, ::Pages)
 
   public fun countUnloadedPages(): Query<Long> = Query(-58_485_640, arrayOf("pages"), driver, "SteleDatabase.sq", "countUnloadedPages", "SELECT COUNT(*) FROM pages WHERE is_content_loaded = 0") { cursor ->
     cursor.getLong(0)!!
@@ -5882,7 +5886,7 @@ public class SteleDatabaseQueries(
 
     override fun <R> execute(mapper: (SqlCursor) -> QueryResult<R>): QueryResult<R> {
       val section_idIndexes = createArguments(count = section_id.size)
-      return driver.executeQuery(null, """SELECT pages.uuid, pages.name, pages.namespace, pages.file_path, pages.created_at, pages.updated_at, pages.properties, pages.version, pages.is_favorite, pages.is_journal, pages.journal_date, pages.is_content_loaded, pages.backlink_count, pages.section_id FROM pages WHERE is_content_loaded = 0 AND section_id IN $section_idIndexes ORDER BY uuid LIMIT ? OFFSET ?""", mapper, section_id.size + 2) {
+      return driver.executeQuery(null, """SELECT pages.uuid, pages.name, pages.namespace, pages.file_path, pages.created_at, pages.updated_at, pages.properties, pages.version, pages.is_favorite, pages.is_journal, pages.journal_date, pages.is_content_loaded, pages.backlink_count, pages.section_id FROM pages WHERE is_content_loaded = 0 AND section_id IN $section_idIndexes ORDER BY uuid LIMIT ? OFFSET ?""", mapper, 2 + section_id.size) {
             var parameterIndex = 0
             section_id.forEach { section_id_ ->
               bindString(parameterIndex++, section_id_)

kmp/src/generated/sqldelight/dev/stapler/stelekit/db/kmp/SteleDatabaseImpl.kt

@@ -266,6 +266,7 @@ private class SteleDatabaseImpl(
       driver.execute(null, "CREATE INDEX idx_pages_created_at ON pages(created_at DESC)", 0).await()
       driver.execute(null, "CREATE INDEX idx_pages_favorite ON pages(name) WHERE is_favorite = 1", 0).await()
       driver.execute(null, "CREATE INDEX idx_pages_journal_section ON pages(is_journal, journal_date, section_id)", 0).await()
+      driver.execute(null, "CREATE INDEX idx_pages_section_id ON pages(section_id, name)", 0).await()
       driver.execute(null, "CREATE INDEX idx_changelog_graph_status ON migration_changelog(graph_id, status)", 0).await()
       driver.execute(null, "CREATE INDEX idx_changelog_applied_at ON migration_changelog(graph_id, applied_at)", 0).await()
       driver.execute(null, """

kmp/src/iosMain/kotlin/dev/stapler/stelekit/sections/SectionManifestTomlDecoder.ios.kt

@@ -0,0 +1,13 @@
+package dev.stapler.stelekit.sections
+
+import com.akuleshov7.ktoml.Toml
+import com.akuleshov7.ktoml.TomlInputConfig
+import kotlinx.serialization.serializer
+
+private val sectionToml = Toml(inputConfig = TomlInputConfig(ignoreUnknownNames = true))
+
+internal actual fun decodeSectionManifestToml(content: String): SectionManifest? =
+    sectionToml.decodeFromString(serializer<SectionManifest>(), content)
+
+internal actual fun encodeSectionManifestToml(manifest: SectionManifest): String =
+    sectionToml.encodeToString(serializer<SectionManifest>(), manifest)

kmp/src/jvmCommonMain/kotlin/dev/stapler/stelekit/sections/SectionManifestTomlDecoder.jvm.kt

@@ -0,0 +1,13 @@
+package dev.stapler.stelekit.sections
+
+import com.akuleshov7.ktoml.Toml
+import com.akuleshov7.ktoml.TomlInputConfig
+import kotlinx.serialization.serializer
+
+private val sectionToml = Toml(inputConfig = TomlInputConfig(ignoreUnknownNames = true))
+
+internal actual fun decodeSectionManifestToml(content: String): SectionManifest? =
+    sectionToml.decodeFromString(serializer<SectionManifest>(), content)
+
+internal actual fun encodeSectionManifestToml(manifest: SectionManifest): String =
+    sectionToml.encodeToString(serializer<SectionManifest>(), manifest)

kmp/src/wasmJsMain/kotlin/dev/stapler/stelekit/sections/SectionManifestTomlDecoder.js.kt

@@ -0,0 +1,8 @@
+package dev.stapler.stelekit.sections
+
+// ktoml generates invalid WASM bytecode (wasm-opt validation failure) — return null
+// so SectionManifestParser falls back to an empty SectionManifest in the browser.
+internal actual fun decodeSectionManifestToml(content: String): SectionManifest? = null
+
+internal actual fun encodeSectionManifestToml(manifest: SectionManifest): String =
+    throw UnsupportedOperationException("TOML encoding not supported on WASM")