Overview

This index catalogs all org-mode literate programming files in the repository and their tangle targets. It is automatically maintained by the Index Agent.

• Total org files scanned: 107 (excluding node_modules, build/, .git/, orgmode-kmp); 64 project files + 43 org-fc fixtures

• Org files producing real .kt tangle targets: 45

• Org files producing any tangle targets: 50 (including .el, .md, .sq, .gradle, .kts, .nix, .json, Makefile, .peb, .css, .js)

• Unique .kt tangle targets: 245

• Unique non-.kt tangle targets: 51 (6 .sq, 6 .nix, 2 .gradle, 2 .kts, 1 Makefile, 2 .el, 10 .md incl. AGENTS.md + 9 agent .md, 12 .peb, 7 .css, 2 .js, 1 .json)

• Orphaned .kt files (no matching :tangle): 4 project files (1 src/jvmTest integration test + 3 app/src/test doubles/tests) + 27 orgmode-kmp = 31 total

• Non-tangled binary assets in src/jvmMain/resources/static/ (NOT orphans — copied directly, can't be tangled from org): highlight.min.js, htmx.min.js, sigma.min.js, graphology.min.js, graphology-library.min.js, fonts/, hljs/ (see web/templates.org and web/sitemap.org narrative)

• Org files producing .sq tangle targets: 6 (roam/models, quiz/models, arroyo/generators, agenda/models, web/publishing, web/feeds)

• Org files producing .md tangle targets: 1 (arroyo/tools → 10 .md files)

• Org files producing .el tangle targets: 1 (arroyo/emacs-integration → lisp/arroyo.el + ~/nix/lisp/arroyo.el)

• Org files producing Makefile tangle targets: 1 (app/cli)

• Org files producing build-system tangle targets: 1 (app/build → 8 files)

• Org files producing .peb/.css/.js static resource targets: 2 (web/templates → 8 .peb + 6 .css + 1 .js; web/sitemap → 4 .peb + 1 .css + 1 .js under static/sitemap/)

• Org files producing .json tangle targets: 1 (web/domains → 1 lua-generated domains.json)

Org File Index

Tracking the decomposition of monolithic source blocks into noweb-composed format (#+name: blocks, :noweb-ref tests, :noweb yes assembly).

Tangle Reverse Map

Orphaned Source Files

These .kt files exist in the source tree but have no matching :tangle directive in any .org file (excluding build/ generated files, excluding orgmode-kmp/).

By Directory

Orphaned Files in src/commonMain/ (0 files)

All src/commonMain domain-logic files are now documented in literate org files.

Orphaned Files in src/jvmMain/ (0 files)

All src/jvmMain files are now documented in literate org files.

Orphaned Files in app/src/main/ (0 files)

All app/src/main UI and component files are now documented in literate org files.

Orphaned Files in app/src/test/ (3 files)

These test doubles and unit tests exist on disk but have no matching :tangle directive. They were previously listed as "documented" in an older index revision, but a fresh scan of #+begin_src :tangle directives in all .org files confirms no org file actually tangling these targets. Candidates for new literate documentation (e.g. a app/test-doubles.org or editor/components-test.org):

• app/src/test/.../app/testutils/AppPreferencesTestDouble.kt

• app/src/test/.../app/testutils/RoamRepositoryTestDouble.kt

• app/src/test/.../app/ui/components/NodeBreadcrumbTest.kt

Orphaned Files in src/commonTest/ (0 files)

All src/commonTest files are now documented in literate org files.

Other Orphaned Areas

• src/jvmTest/ (1 file): RealOrgRoamIntegrationTest.kt (integration test that directly references the org-roam repo on disk, single large file)

• orgmode-kmp/ (27 files): External library, separate project. Includes the recently directly-edited OrgLogbook.kt and OrgLogbookTest.kt (orgmode-kmp/orgmode/src/commonMain/kotlin/xyz/lepisma/orgmode/... and .../commonTest/...), which have no :tangle mapping in any project .org file. These edits live outside the literate workflow and are not tracked by the index beyond this orphan flag.

Related Org Files (Non-Tangle)

These org files were scanned but do not produce tangle targets:

• app/index.org — Android App Development Index (ID: 20260530T210000.000001)

• agenda/index.org — Agenda Feature (parent index for the agenda/* cluster: models.org, indexer.org, habits.org, screen.org)

• vision/index.org — Arcology Vision (ID: 20260530T210000.000002)

• arroyo/arroyo.org — Arroyo Literate Programming Environment (ID: 20260605T120149.238785)

• web/index.org — Arcology Web Publishing Plan

• desktop/index.org — Linux Desktop Port - Development Plan

• MODAL_KEYBOARD_DESIGN.org — Modal Keyboard Navigation Design (superseded by editor/screen.org)

• vision/features.org — Feature requirements (ID: 20251212T231404.213411)

• vision/requirements.org — Requirements

• vision/international-trip.org — The International Trip (ID: f3130092-832d-42c2-8e8b-d467ceefac07)

• contributing.org — Development guidelines

• README.org — The Arcology Project

• LICENSE.org — License

• orgmode-kmp/orgmode/src/docs/org_test.org — Org Test (ID: 21e2c8f6-8dbb-4002-bcf5-a15203516114)

• orgmode-kmp/README.org — orgmode-kmp

• org-fc/ (43 files) — Org-flashcard test fixtures and documentation

Agent Metadata

• Generated: 2026-05-21

• Updated: 2026-09-09 (Phase 5 — Feed Publishing + sitemap re-scan)

  • NEW web/feeds.org (ID 20260908T090000.000001, ARCOLOGY_KEY arcology/web/feeds). 10 tangle targets (9 .kt + 1 .sq), all :noweb yes assembly blocks over named #+name: fragments: src/commonMain/sqldelight/computer/whatthefuck/arcology/db/Feeds.sq (feeds declarer rows keyed (route_key, file) + feed_entries), FeedModels.kt (=FeedModel=/=FeedEntryModel=), PubdateParser.kt (org timestamp → RFC-3339 UTC), FeedRepository.kt (interface + FeedRepositoryImpl), ArcologyFeedPlugin.kt (indexer plugin doing the PUBDATE property rollup), FeedPublisher.kt (serve-time aggregator, top-10 by pubdate), plus 4 tests PubdateParserTest.kt ArcologyFeedPluginTest.kt (commonTest) and FeedRepositoryTest.kt FeedPublisherTest.kt (jvmTest).

  • web/server.org: 3 NEW tangle targets. src/jvmMain/.../publishing/NodeRendering.kt (shared node-body pipeline: loadNodeParseResult renderParsedNode + hoisted top-level findSectionByNodeId, reused by FeedPublisher for one-parse-N-renders) and 2 new jvmTest targets ArcologyServerRouteLookupTest.kt + ArcologyServerFirstRenderTest.kt (fixture org file + fake repos). Also ArcologyServer.kt gained top-level opmlFor opmlEscape (GET /opml.xml OPML feed-list route, commit 6a7a70e) — same file, no new target. Tangle target count: 5 .kt + 3 test .kt → 6 .kt + 5 test .kt. The ServeCommand.kt target path moved package arcology/cli → arcology/publishing (same tangle target file, renamed — on-disk confirmed both cli/ArcologyCli.kt and publishing/ServeCommand.kt exist; the old cli/ServeCommand.kt no longer exists).

  • web/sitemap.org: PREVIOUSLY UNINDEXED (created 2026-09-01, after the 2026-08-26 index update — pre-existing drift, not Phase 5). Added to Org File Index + reverse map: 2 jvmMain .kt (SitemapGraph.kt, TagIndex.kt) + 1 jvmTest .kt (SitemapTest.kt) + 4 .peb (graph, tags, tag, tag-list) + static/sitemap/sitemap.css + static/sitemap/graph.js. DONE (noweb assemblies: sitemap-graph-assembly, tag-index-assembly, sitemap-test-assembly).

  • web/templates.org: sidebar.peb tangle target REPLACED by topic.peb (commit a90cef6 "better page templates"; sidebar.peb remains on disk as an included partial but is no longer tangled — its five panels are now =:noweb-ref sidebar-= fragments woven into page.peb wide.peb topic.peb). Count unchanged 8 .peb + 6 .css + 1 .js. - web/index.org: route table + Phase 5 marked DONE (narrative edit, no tangle targets — index-org files produce none). - roam/indexer-platform.org: NO new tangle targets. FlowFileIndexerFactory.kt now registers ArcologyFeedPlugin(feedRepository) alongside ArcologyAttachmentPlugin. Count unchanged (4 .kt). - Orphaned .kt count UNCHANGED: 4 project files (1 src/jvmTest RealOrgRoamIntegrationTest.kt + 3 app/src/test test doubles/tests) + 27 orgmode-kmp = 31 total. All 10 new feed targets and NodeRendering.kt were created with matching :tangle directives in the same session — none entered the orphan list. Verified by full comm() scan: 249 .kt files on disk, 245 mapped unique .kt targets, exactly 4 orphans. - Unique .kt tangle targets: 230 → 245 (+15: 9 feeds + 3 server + 3 sitemap). - Unique non-.kt tangle targets: 44 → 51 (+7: +1 .sq Feeds.sq, +4 .peb sitemap, +1 .css, +1 .js; −1 .peb sidebar → +1 .peb topic in templates). - Org files producing .kt tangle targets: 43 → 45 (+2: web/feeds.org, web/sitemap.org). - Org files producing any tangle targets: 48 → 50 (+2). - Org files producing .sq tangle targets: 5 → 6 (+1: web/feeds). - Org files producing .peb/.css/.js static targets: 1 → 2 (+1: web/sitemap). - Total org files scanned: 105 → 107 (+2: web/feeds.org, web/sitemap.org). - Updated: 2026-08-26 (Phase 4 — Attachment Handling) - web/publishing.org: 4 NEW tangle targets added (Phase 4 Attachment Handling section): src/jvmMain/.../publishing/AttachmentCrusher.kt (named block tangling the attachment image-crush pipeline — imagemagick-driven resize/optimization), src/jvmMain/.../publishing/ArcologyAttachmentPlugin.kt (IndexerPlugin that indexes published attachments into the new published_attachments table), src/jvmTest/.../publishing/AttachmentCrusherTest.kt, src/jvmTest/.../publishing/ArcologyAttachmentPluginTest.kt. All 4 are :noweb yes assembly blocks consistent with the file's existing structure. Tangle target count: 7 commonMain .kt + 4 commonTest .kt → 9 .kt (7 commonMain + 2 jvmMain) + 6 test .kt (4 commonTest + 2 jvmTest); .sq unchanged (the existing Publishing.sq block gained the published_attachments schema/queries — same file, modified content, no new target). - web/renderer.org: NO new tangle targets. LinkResolver.kt block modified (added AttachmentRef + resolveAttachment); OrgHtmlRenderer.kt block modified (added attachment branch in renderLink + renderImageAttachment, emitting htmx hx-get / =hx-swap="outerHTML"= for progressive enhancement). The OrgHtmlRendererTest.kt block gained an "image attachment link renders img with htmx swap" test. Count unchanged (2 .kt + 1 test .kt). is-restructured remains DONE. - web/server.org: NO new tangle targets. ArcologyServer.kt, PageModel.kt, CrossDomainLinkResolver.kt, ServeCommand.kt, CrossDomainLinkResolverTest.kt, NestedSectionLookupTest.kt blocks modified to wire attachment routes / page models. Count unchanged (5 .kt + 3 test .kt). is-restructured remains DONE. - roam/indexer-platform.org: NO new tangle targets. FlowFileIndexerFactory.kt block modified to register ArcologyAttachmentPlugin in the plugin list. Count unchanged (4 .kt). - roam/models.org: NO new tangle targets. DatabaseFactory.kt block modified (db-factory self-heal on schema mismatch). Count unchanged (15 .kt + 1 .sq). - web/templates.org: NO new tangle targets. app.peb block modified — added =<script src="/static/htmx.min.js" defer></script=. The htmx.min.js file itself is a binary asset copied directly into src/jvmMain/resources/static/ (v2.0.4), NOT tangled from org — same convention as highlight.min.js, =fonts/=, =hljs/= (already noted in the web/templates.org narrative at line 26). It does NOT appear in the orphan list: the index orphans section tracks only .kt files, and non-tangled static assets are excluded by convention. Count unchanged (8 .peb + 6 .css + 1 .js). - app/build.org: NO new tangle targets. build.gradle.kts block modified (added ktor-server-conditional-headers dep, restored ktor-server-pebble); default.nix block modified (added imagemagick runtime dep + makeBinPath for the attachment crusher). Count unchanged (8 build targets). - app/cli.org: NO new tangle targets. Makefile block modified (update-deps target fix → mitmCache.updateScript). Count unchanged (2 .kt + 1 Makefile). - gradle/libs.versions.toml and shell.nix: edited directly, NOT tangled from any project .org file. shell.nix header points to a journal file (../../org/journals/2025-12-28.org), not a project org file. Both are outside the literate workflow and not tracked by this index beyond this note (the index only catalogs :tangle targets and .kt orphans). - Orphaned .kt count UNCHANGED: 4 project files (1 src/jvmTest RealOrgRoamIntegrationTest.kt + 3 app/src/test test doubles/tests) + 27 orgmode-kmp = 31 total. All 4 new attachment files (AttachmentCrusher.kt, ArcologyAttachmentPlugin.kt, AttachmentCrusherTest.kt, ArcologyAttachmentPluginTest.kt) were created with matching :tangle directives in the same session — none entered the orphan list. Verified on disk: both =src/jvmMain/.../publishing/={AttachmentCrusher,ArcologyAttachmentPlugin}.kt= and =src/jvmTest/.../publishing/={AttachmentCrusher,ArcologyAttachmentPlugin}Test.kt= exist and are mapped. - Unique .kt tangle targets: 226 → 230 (+4: the 4 new attachment .kt files). - Unique non-.kt tangle targets: 44 (unchanged — the Publishing.sq modification adds queries to an already-counted target, not a new file). - Org files producing .kt tangle targets: 43 (unchanged — web/publishing.org was already a producer). - Org files producing any tangle targets: 48 (unchanged). - Added overview bullet noting non-tangled binary assets (highlight.min.js, htmx.min.js, =fonts/=, =hljs/=) for discoverability, consistent with the existing web/templates.org narrative convention. - Updated: 2026-07-13 (arroyo emacs expansion) - arroyo/emacs-integration.org: package.el header added to arroyo-emacs block; new arroyo-mode global minor mode (menu-bar on org-mode-map, tool-bar button for arroyo-flood, disables legacy org-auto-tangle-mode); new "Emacs Package Derivation" heading → emacs-pkg.nix (trivialBuild of lisp/arroyo.el, callPackage'd by flake); new "Arroyo Emacs Module" heading (ARROYO_EMACS_MODULE: arroyo, ARROYO_MODULE_WANTS: cce/literate_programming) → ~/nix/lisp/arroyo.el (use-package arroyo :ensure t + arroyo-mode); new "Arroyo Epkg Override" heading (ARROYO_HOME_EPKGS: overrides/arroyo.nix) → ~/nix/overrides/arroyo.nix (references inputs.arcology2go.emacsPackages.${system}.default). Tangle target count: 1 .el → 1 .el + 1 .nix + 2 ~/nix (4 total). - app/build.org: flake.nix source block updated — added emacsPackages.default pkgs.callPackage ./emacs-pkg.nix {}= alongside packages.default. Tangle target count unchanged (8). - Unique non-.kt tangle targets: 23 → 26 (+3: emacs-pkg.nix, ~/nix/lisp/arroyo.el, ~/nix/overrides/arroyo.nix). - New tangle targets registered in reverse map under arroyo/emacs-integration. - Updated: 2026-06-30 (nested .arcologyignore support) - roam/indexer.org: IgnorePatterns source block (tangles to IgnorePatterns.kt) rewritten for nested-scope semantics; IgnorePatternsTest block (tangles to IgnorePatternsTest.kt) rewritten with anchored-semantics + nested-scope tests; FlowFileIndexer loadIgnorePatterns doc comment updated; "Ignore Patterns" narrative expanded. Tangle target count unchanged (6 .kt). - roam/indexer-platform.org: JvmFileSystem block walkWithIgnorePatterns rewritten to read nested .arcologyignore files during traversal; AndroidFileSystem block emitOrgFilesEfficient rewritten to detect/accumulate nested .arcologyignore scopes; new jvm-nested-ignore-test named block added (tangles to src/jvmTest/.../indexer/JvmFileSystemNestedIgnoreTest.kt) with "JVM Walker Tests" section. Tangle target count: 3 .kt → 4 .kt (+1). - New tangle target registered: src/jvmTest/kotlin/computer/whatthefuck/arcology/indexer/JvmFileSystemNestedIgnoreTest.kt → roam/indexer-platform.org (was a new on-disk file from this session, now mapped — no longer a candidate orphan). - Orphaned .kt count unchanged: 4 project files (1 src/jvmTest integration test RealOrgRoamIntegrationTest.kt + 3 app/src/test test doubles/tests) + 25 orgmode-kmp = 29 total. The new JvmFileSystemNestedIgnoreTest.kt was created and mapped in the same session, so it never entered the orphan list. - Unique .kt tangle targets: 195 → 196 (+1). - Org files producing .kt tangle targets: 44 → 44 (no change; roam/indexer-platform.org already produced .kt). - Updated: 2026-06-29 (arcology2go flake + Arroyo HM module) - Added flake.nix to app/build.org tangle targets (wraps default.nix as packages.default / apps.default so the repo can be used as a flake input). - app/build.org now declares ARROYO_INPUT: snippets/arcology2go-input.nix (file-level) and ARROYO_HOME_MODULE: hm/arcology2go.nix (role-scoped to endpoint server settop edge) — the Arroyo indexer picks these up and the Arroyo System Flake Generator composes them, putting the stable arcology CLI in PATH on every home-manager role. - app/build.org build target count: 5 → 6 (added flake.nix). - Follow-up: added two missing Tangle Reverse Map rows for the Arroyo integration targets declared above — ~/nix/snippets/arcology2go-input.nix (flake input snippet, :tangle ~/nix/snippets/arcology2go-input.nix) and ~/nix/hm/arcology2go.nix (Home Manager module, :tangle ~/nix/hm/arcology2go.nix, heading ID arcology2go-hm, ARROYO_SYSTEM_ROLE: endpoint server settop edge). Both tangle out of the = Arroyo System Integration= section of app/build.org.

  • app/build.org build target count: 6 → 8 (added snippets/arcology2go-input.nix + hm/arcology2go.nix). Unique non-.kt tangle targets: 22 → 24 (+2 .nix).

• Updated: 2026-06-24 (post-arroyo2-merge full re-scan)

  • Full re-scan of all 103 .org files (60 project + 43 org-fc) against live #+begin_src :tangle directives; excluded escaped/illustrative lines (lines beginning with ,#+begin_src) and test-fixture targets (src/Out.kt, src/File.kt, flake.nix, result.nix in arroyo/tests.org) that exist only inside Kotlin raw-string test inputs.

  • Corrected roam/models.org count: 14 .kt → 15 .kt (added IndexerPlugin.kt)

  • Corrected agenda/tasks.org count: 3 .kt → 4 .kt (added TaskIndexerPlugin.kt)

  • Corrected quiz/flashcard.org count: 6 .kt → 7 .kt (added QuizIndexerPlugin.kt)

  • Corrected arroyo/core.org count: 15 .kt → 16 .kt (added ArroyoTangleContext.kt)

  • Corrected arroyo/generators.org count: 10 .kt → 9 .kt (prior count was overstated)

  • Corrected find/map-screen.org count: 4 .kt → 6 .kt (added MapUtils.kt, OsmTileProvider.kt)

  • Corrected find/graph-screen.org count: 2 .kt → 5 .kt (added GraphControls.kt, GraphNodeComposable.kt, KuiverGraphView.kt)

  • Corrected agenda/data.org count: 2 .kt → 1 .kt (only TasksRepository.kt + Tasks.sq; prior count was overstated)

  • Added roam/parser.org to the Org File Index table (ID 20260520T173000.000001, 11 .kt targets) — was previously missing from the summary table

  • Rebuilt full reverse map (216 entries, 195 unique .kt + 22 non-.kt) grouped by source area

  • Orphaned .kt count corrected: 1 → 4 project files. The 3 app/src/test files (AppPreferencesTestDouble.kt, RoamRepositoryTestDouble.kt, NodeBreadcrumbTest.kt) previously listed as "documented" are in fact NOT referenced by any :tangle directive and are genuine orphans awaiting literate documentation. RealOrgRoamIntegrationTest.kt remains an intentional orphan.

  • Removed stale references from Related Org Files: duplicate desktop/index.org line, missing context/2026-03-19.org and context/pu_lesson_15.org, and arroyo/tools.org (it IS a tangle producer, 9 .md targets).

  • Added app/index.org, vision/index.org, arroyo/arroyo.org to Related Org Files.

  • Unique .kt tangle targets: 192 → 195 (+3)

  • Org files producing .kt tangle targets: 44 → 44 (no change; counts within files corrected)

  • Orphaned count: 26 → 29 (+3 net: +3 project, +0 orgmode-kmp)

  • Added roam/fixtures.org (ID 20260601T130000.000001, 3 .kt targets): SampleOrgFiles.kt, TestData.kt, OrgContentGenerators.kt

  • Added IgnorePatternsTest.kt to roam/indexer.org (now 6 .kt targets)

  • Added FlowTestUtils.kt, FlowIndexingTest.kt, AttachmentIndexingTest.kt, AttachmentResolverTest.kt, FlowFileIndexerTimeoutTest.kt, FlowOomTest.kt to roam/indexer-test.org (now 8 .kt targets)

  • Added HeadingTextUtilsTest.kt, HeadingTextUtilsPropertyTest.kt, OrgDocumentEditorTest.kt, PropertyDrawerUtilsTest.kt, ReviewDataDrawerUtilsTest.kt to roam/editor.org (now 10 .kt targets)

  • Added ModelsTest.kt, RoamRepositoryTest.kt to roam/models.org (now 14 .kt targets)

  • Added AnchorExtractorTest.kt to arroyo/core.org (now 15 .kt targets)

  • Removed 18 src/commonTest files from orphan list (all now documented)

  • Orphaned count: 57 → 35 (-22) — 10 project + 25 orgmode-kmp

  • Unique .kt tangle targets: 155 → 177 (+22)

  • Org files producing .kt tangle targets: 39 → 42 (+3)

• Updated: 2026-05-30

  • Added app/onboarding-indexing.org (ID 20260529T000001, 4 .kt targets): IndexingViewModel.kt, OnboardingScreen.kt, IndexingScreen.kt, IndexingViewModelTest.kt

  • Added app/settings-screen.org (ID 20260529T000002, 1 .kt target): SettingsScreen.kt

  • Added InlineHeadingText.kt and TaskListItem.kt to agenda/agenda-screen.org (now 4 .kt targets)

  • Added OrgVisualTransformation.kt to editor/body-editor.org (now 2 .kt targets)

  • Added TemplateSettingsScreen.kt to editor/components.org (now 5 .kt targets)

  • Added LinkParser.kt and OrgStringBuilder.kt to editor/renderer.org (now 9 .kt targets)

  • Confirmed deletion: EditorViewModel.kt, OrgContentRenderer.kt, CollapsedNodeCard.kt, FiletagPicker.kt, FontUtils.kt

  • Removed IndexingViewModel.kt, IndexingScreen.kt, OnboardingScreen.kt, SettingsScreen.kt, InlineHeadingText.kt, OrgVisualTransformation.kt, TemplateSettingsScreen.kt, LinkParser.kt, OrgStringBuilder.kt, TaskListItem.kt from orphan lists (now documented)

  • Removed IndexingViewModelTest.kt from app/src/test orphan list

  • Orphaned count: 81 → 57 (-24) — 32 project + 25 orgmode-kmp

  • Unique .kt tangle targets: 135 → 155 (+20)

  • Org files producing .kt tangle targets: 34 → 39 (+5)

• Updated: 2026-06-11 (Sprint 5)

  • Added arroyo/emacs-integration.org (ID 20260611T120000.000001, 1 .el target): lisp/arroyo.el

  • Added arroyo/generators.org (ID 20260607T120000.000001, 10 .kt + 1 .sq targets): ArroyoScriptHost.kt, TopologicalSort.kt, GeneratorCommands.kt, Arroyo.sq, ArroyoRepository.kt, ArroyoIndexerPlugin.kt, ArroyoIndexingTest.kt, ArroyoQueryTest.kt, RealArroyoIntegrationTest.kt, ArroyoIndexerPluginTest.kt

  • Added FloodCommandTest.kt to arroyo/tests.org (now 3 .kt targets)

  • Updated roam/cli.org — registered FloodCommand, added make flood target

  • Updated arroyo/generators.org — added FloodCommand class, matchesRole() utility

  • Updated arroyo/arroyo.org — Sprint 5 documentation

  • Removed 10 arroyo source files from orphan list (all now documented in arroyo/generators.org)

  • Orphaned count: 57 → 26 (-31) — 1 project + 25 orgmode-kmp

  • Unique .kt tangle targets: 177 → 192 (+15)

  • Org files producing .kt tangle targets: 42 → 44 (+2)

  • New tangle target type: .el (Emacs Lisp)

• Updated: 2026-07-03 (CLI refactor re-scan)

  • Full re-scan of all 99 .org files (56 project + 43 org-fc) against live #+begin_src :tangle directives; excluded escaped lines (leading , before #+begin_src), markdown ```-fenced illustrative blocks (e.g. the src/File.kt examples in arroyo/tools.org), and the src/Out.kt test-fixture target in arroyo/tests.org (a non-escaped #+begin_src line inside a Kotlin raw-string OrgDetangle.detangle() test input that is never written to disk). The flake.nix references in arroyo/tests.org are comma-escaped and already skipped; the real flake.nix is produced by app/build.org.

  • roam/cli.org DELETED in commit fd3b23f; its Makefile + ArcologyCli.kt tangle targets moved to a NEW file app/cli.org (ID 20260520T200000.000001, same ID carried over from roam/cli.org). Org File Index row relocated from the roam/ group to the app/ group; Tangle Reverse Map section renamed =— roam/cli — → — app/cli —=.

  • roam/indexer.org gained a new "CLI Commands" section (heading ID 20260702T220547.974545) with 5 source blocks all tangling to ../src/jvmMain/kotlin/computer/whatthefuck/indexer/IndexerCommands.kt. roam/indexer.org tangle target count: 6 .kt → 7 .kt (+1). New reverse-map row: src/jvmMain/.../indexer/IndexerCommands.kt → roam/indexer.org.

  • mcp/server.org + mcp/tools.org DELETED in commit fd3b23f along with their tangled targets ArcologyMcpServer.kt, HttpTransport.kt, StdioTransport.kt, SearchTool.kt. McpCommand.kt (formerly in =roam/cli.org='s reverse map) also DELETED. All five .kt targets removed from the reverse map.

  • Net deltas measured by this scan: org files producing .kt tangle targets 44 → 40 (-4: -3 deleted mcp/server.org, mcp/tools.org, roam/cli.org; +1 added app/cli.org; note the prior "44" count was itself slightly overstated relative to the live tree); unique .kt tangle targets 196 → 192 (-4: -5 deleted MCP targets +1 added IndexerCommands.kt); org files producing any tangle targets 46 → 43 (-3: -3 deleted producers +0, since app/cli.org replaces roam/cli.org and roam/indexer.org was already a producer); total org files scanned 103 → 99 (60 → 56 project files; the prior "60 project" figure was stale — earlier commits had also deleted AGENDA_PLAN.org, ANDROID_APP_PLAN.org, ARROYO_APP_PLAN.org, LLM_APP_PLAN.org, literate-re.org, literate-re/literate-re-cli.org, roam.org).

  • Orphaned .kt count unchanged: 4 project files (1 src/jvmTest RealOrgRoamIntegrationTest.kt + 3 app/src/test test doubles/tests) + 25 orgmode-kmp 29 total. The CLI refactor neither added nor removed any on-disk .kt without a matching :tangle=.

  • Unique non-.kt tangle targets: 24 → 23 (-1: the flake.nix fixture in arroyo/tests.org was previously double-counted in the overview bullet; the real flake.nix from app/build.org is the only one. Breakdown: 4 .sq, 4 .nix, 2 .gradle, 2 .gradle.kts, 1 Makefile, 1 .el, 9 .md).

• Agent: Index Agent (arcology2go)

• Command: update-index → Full re-scan with live :tangle verification (post-arroyo2-merge)

• Updated: 2026-08-25 (publishing2 branch — web cluster expansion)

  • Full re-scan of all 105 .org files (62 project + 43 org-fc) against live #+begin_src :tangle directives; excluded comma-escaped illustrative lines and the known ../src/File.kt false positive inside =arroyo/tools.org='s markdown agent-doc blocks (a nested example, not a real tangle target).

  • web/ cluster expanded from 1 file to 5 files; ~28 new tangle targets registered from the branch:

    • web/server.org: expanded from "1 .kt (WIP) NOT DONE" to 5 .kt (ArcologyServer.kt, PageModel.kt, HtmlCache.kt, CrossDomainLinkResolver.kt, ServeCommand.kt) + 3 jvmTest .kt (HtmlCacheTest.kt, NestedSectionLookupTest.kt, CrossDomainLinkResolverTest.kt). is-restructured NOT DONE → DONE (fully :noweb yes assembly with :noweb-ref server-imports server-method fragments).

    • web/publishing.org: NEW (ID 20260710T100000.000001). 7 commonMain .kt (PublishKey.kt, DomainMap.kt, RouteTable.kt, PublishingRepository.kt, RouteTableBuilder.kt, ExcludeTags.kt, ArcologyPublishingPlugin.kt) + 1 .sq (Publishing.sq) + 4 commonTest .kt. DONE (:noweb yes assembly with named #+name: phase blocks). [Prompt claimed "8 .kt" — actual scan finds 7 commonMain .kt; the prompt overcounted by 1.]

    • web/renderer.org: NEW (ID 20260710T110000.000001). 2 commonMain .kt (LinkResolver.kt, OrgHtmlRenderer.kt) + 1 commonTest .kt (OrgHtmlRendererTest.kt). DONE (:noweb yes assembly with #+name: inline-renderer block-renderer section-renderer fragments).

    • web/templates.org: NEW (ID 20260721T120000.000001). 15 static resource targets: 8 .peb (app, page, wide, sidebar, 404, sitemap, feed, robots) + 6 .css (arcology.css, vulf.css, arcology/css/{lionsrear,garden,cce,arcology-engine}.css) + 1 .js (arcology-src-blocks.js). NOT DONE (flat named blocks, no noweb composition). [Prompt said "~16 static resources" — actual scan finds 15.]

    • web/domains.org: NEW (ID 20260710T130000.000001). 1 .json target (web/domains.json) generated by a :eval arroyo lua block from the site-meta org table. NOT DONE.

  • New reverse-map sections added: web/domains, web/publishing, web/renderer, web/server, web/templates (the old index had no web/server reverse-map rows — the WIP file was table-only).

  • Pre-existing index inaccuracies corrected by the fresh scan (not from publishing2 — these were already wrong on main):

    • agenda/notifications.org (ID 20260811T000001, 4 .kt) was entirely missing from the old index (both table and reverse map). Added to the agenda section (now 6 files) with reverse-map rows for TaskReminderWorker.kt, TaskNotificationManager.kt, HabitReminderWorker.kt, HabitNotificationManager.kt.

    • quiz/flashcard.org: 7 .kt → 10 .kt (+3 previously-missed targets: ReviewHistoryWriter.kt, ReviewHistoryWriterTest.kt, QuizIndexerPluginReviewHistoryTest.kt). Reverse-map rows added.

    • roam/parser.org: table said 11 .kt → corrected to 13 .kt (the old reverse map already listed 13 entries; only the table label was wrong). Prompt asked to "confirm 11" — actual is 13.

    • app/data.org: table said 10 .kt → corrected to 9 .kt (the old reverse map already listed 9; only the table label was wrong).

    • arroyo/tools.org: 9 .md → 10 .md (literate-restructure.md was missing from the reverse map). Row added.

    • app/cli.org: reverse map was missing CliProgressReporter.kt (src/jvmMain/.../arcology/cli/CliProgressReporter.kt) — the table count "2 .kt" was correct but the reverse map only listed 1 .kt. Row added.

  • Orphaned .kt count unchanged: 4 project files (1 src/jvmTest RealOrgRoamIntegrationTest.kt + 3 app/src/test test doubles/tests) + 27 orgmode-kmp = 31 total. All new =src/.../publishing/.kt= and =src/jvmTest/.../publishing/Test.kt= files from publishing2 have matching :tangle directives — none entered the orphan list. The CrossDomainLinkResolverTest.kt, HtmlCacheTest.kt, and NestedSectionLookupTest.kt jvmTest files are all mapped to web/server.org.

  • Before → after (old overview stated → actual scan): Unique .kt tangle targets 207 → 226 (+19); Unique non-.kt tangle targets 27 → 44 (+17: +1 .sq, +1 .nix correction, +1 .md, +8 .peb, +6 .css, +1 .js, +1 .json); Org files producing any tangle targets 47 → 48 (+1 net: +4 new web/ producers, but the old "47" had itself understated agenda/notifications.org which is now counted). Note: the old overview's "207" "27" "47" figures had pre-existing internal inconsistencies (the old reverse map actually listed only 198 .kt entries, not 207), so the raw deltas mix publishing2 additions with corrections of old drift.

• Updated: 2026-08-06 (agenda feature + roam/editor expansion)

  • Added the new agenda/ feature cluster (4 tangle-producing org files + 1 parent index):

    • agenda/models.org (ID 20260731T210000.000001, 4 .kt + 1 .sq): TaskHeading.kt, AgendaRepository.kt, Agenda.sq, TaskModelsTest.kt, AgendaRepositoryTest.kt. Notable named blocks: agenda-models-task-heading, agenda-models-task-timestamp, agenda-models-task-state-change, db-agenda-schema, db-agenda-queries, agenda-repo-interface, agenda-repo-impl-header, task-models-test, agenda-repository-test. The TaskHeading model embeds TaskTimestamp and TaskStateChange; the AgendaRepository covers tasks/agenda/projects/history with a transaction wrapper.

    • agenda/indexer.org (ID 20260731T220000.000001, 2 .kt): TaskIndexerPlugin.kt (named block task-indexer-plugin) + TaskIndexerPluginTest.kt. Plugin walks the org AST to populate task_headings with repeater expansion, scheduled/deadline timestamps, and habit detection; supports timestamp deletion on heading removal.

    • agenda/habits.org (ID 20260805T120000.000001, 2 .kt + 1 test .kt): HabitViewModel.kt, HabitScreen.kt, HabitViewModelTest.kt. ViewModel surfaces habit day-state computations (HabitItem HabitDay HabitDayState), screen renders cards with sparklines (HabitCard, HabitSparkline, HabitScreen).

    • agenda/screen.org (ID 20260803T200000.000001, 2 .kt + 1 test .kt): AgendaViewModel.kt, AgendaScreen.kt, AgendaViewModelTest.kt. ViewModel pulls tasks/agenda from AgendaRepository; screen renders AgendaItemCard entries and hosts the four-tab TabRow (Agenda, Habits, Projects, Tagged).

    • agenda/projects.org (ID 20260807T200000.000001, 2 .kt + 3 test .kt): ProjectViewModel.kt (defines ProjectViewModel for the by-file Projects tab, TaggedTasksViewModel for the by-tag Tagged tab, shared TaskListViewModel for task-card actions and detail state, ProjectItem data class), ProjectsTabContent.kt (ProjectsTabContent + ProjectDetailScreen + TaggedTasksScreen + TaggedTasksDetailScreen + shared TodoStatePickerDialog + ProjectTaskCard), ProjectViewModelTest.kt, TaskListViewModelTest.kt, TaggedTasksViewModelTest.kt. The by-file view shows files as projects with stuck/retired badges; the by-tag view shows untagged tasks as a meta section then tag-grouped sections with a text filter and drill-in detail.

  • roam/editor.org: 10 .kt → 13 .kt (+3). Added PlanningInfoUtils.kt (named block tangling to src/commonMain/.../editor/PlanningInfoUtils.kt, supports the repeater reschedule + logbook fix work in OrgDocumentEditor), PositionBasedEditorTest.kt (src/commonTest/.../editor/PositionBasedEditorTest.kt), and PlanningInfoUtilsTest.kt (src/commonTest/.../editor/PlanningInfoUtilsTest.kt). OrgDocumentEditor.kt source block remains :noweb yes with position-based method composition.

  • roam/models.org: IndexerPlugin.kt source block now also defines the IndexerPluginFactory class (concrete DI holder distinguishing the plugin-list factory from other =Function1=-shaped Koin singles under R8 type erasure). No new tangle target — same file; count unchanged (15 .kt + 1 .sq).

  • app/bootstrap.org (AppModule.kt): now wires IndexerPluginFactory as a Koin single and resolves it at every FlowFileIndexer construction site (9 references in bootstrap.org, 1 in =app/data.org='s IndexingWorker.kt via inject()). No new tangle target — same AppModule.kt file; count unchanged (6 .kt). HabitViewModel also wired here.

  • app/data.org (IndexingWorker.kt): injected IndexerPluginFactory for plugin list construction during background indexing. No new tangle target — same file; count unchanged (10 .kt).

  • Orphaned .kt count: 4 project + 25 orgmode-kmp 29 → 4 project + 27 orgmode-kmp 31 (+2). The +2 are the directly-edited OrgLogbook.kt and OrgLogbookTest.kt in orgmode-kmp/, which have no :tangle mapping in any project .org file (they live in the external orgmode-kmp library and were edited outside the literate workflow). All 4 agenda source files (TaskIndexerPlugin.kt, TaskIndexerPluginTest.kt, AgendaViewModel.kt, AgendaViewModelTest.kt, HabitViewModel.kt, HabitViewModelTest.kt, HabitScreen.kt, AgendaScreen.kt, TaskHeading.kt, AgendaRepository.kt, Agenda.sq, TaskModelsTest.kt, AgendaRepositoryTest.kt) and the 3 new roam/editor files (PlanningInfoUtils.kt, PositionBasedEditorTest.kt, PlanningInfoUtilsTest.kt) were created with matching :tangle directives in the same session, so none entered the orphan list.

  • Unique .kt tangle targets: 192 → 207 (+15: +13 from agenda cluster 2+4+3+3+1 .kt across models/indexer/habits/screen minus .sq, exactly: agenda/models 4 .kt, agenda/indexer 2 .kt, agenda/habits 3 .kt, agenda/screen 3 .kt 12, +3 from roam/editor = 15).

  • Unique non-.kt tangle targets: 26 → 27 (+1: Agenda.sq from agenda/models.org).

  • Org files producing .kt tangle targets: 40 → 44 (+4: agenda/models, agenda/indexer, agenda/habits, agenda/screen).

  • Org files producing any tangle targets: 43 → 47 (+4).

  • Org files producing .sq tangle targets: 3 → 4 (+1: agenda/models).

  • Total org files scanned: 99 → 103 (+4 project files: agenda/models.org, agenda/indexer.org, agenda/habits.org, agenda/screen.org; agenda/index.org already existed as a stub and was reclassified from "Related Org Files" to the agenda cluster parent).