feat: convert lithoglyph from stale gitlink to tracked files + Phase A+B pipeline work

Convert lithoglyph/ from a stale gitlink (commit pointer with no .git)
to fully tracked monorepo files. This was caused by the Feb 20 .git
cleanup removing the nested .git without updating the parent index.

Lithoglyph changes included:
- FormBD → Lith rename complete (292+ files, zero remaining refs)
- formdb-http/ → lith-http/ rename (IP: Google owns "FormDB")
- Zig 0.15.2 HTTP API confirmed complete (77 call sites)
- Bofig evidence collection schema (5 collections + 1 edge collection)
- FQL test vectors for bofig_evidence, claims, entities, transactions
- Cap'n Proto → Lithoglyph ingest bridge (bofig-ingest.sh + .exs)
- Zig lith_adapter (StageResults → JSON with auto-PROMPT scoring)
- Integration plan and Epstein test pathway documentation
- STATE.scm updated to 75% completion
- All FORMDB_* env vars → LITH_* across configs, docs, clients

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: hyperpolymath

lithoglyph

@@ -0,0 +1,27 @@
+;; SPDX-License-Identifier: PMPL-1.0-or-later
+;; Bot Directives - Lithoglyph
+;;
+;; This directory contains directives for the gitbot-fleet automation system.
+;; Bots read these files to understand how to operate on this repository.
+
+(bot-directives
+  (version "1.0")
+  (repo "lithoglyph")
+  (fleet-members
+    "rhodibot"    ; Git operations
+    "echidnabot"  ; Code quality
+    "sustainabot" ; Dependency updates
+    "seambot"     ; Integration checks
+    "finishbot")) ; Task completion
+
+;; Bot Responsibilities:
+;;
+;; rhodibot - Automated git operations (commits, tags, releases)
+;; echidnabot - Code quality enforcement (linting, tests, analysis)
+;; sustainabot - Dependency updates (Zig, Factor, Elixir packages)
+;; seambot - Integration verification (cross-language FFI checks)
+;; finishbot - Task completion tracking (TODOs, milestones)
+
+;; Configuration Format:
+;; Each bot has its own .scm file defining its behavior for this repo.
+;; The format is S-expression based for easy parsing by Scheme/Elixir bots.

lithoglyph/.bot_directives/README.scm

@@ -0,0 +1,47 @@
+;; SPDX-License-Identifier: PMPL-1.0-or-later
+;; Echidnabot Directives - Code Quality Automation
+;;
+;; Echidnabot enforces code quality standards, runs static analysis,
+;; and ensures industrial-grade code for Lithoglyph.
+
+(echidnabot-config
+  (repo-name "lithoglyph")
+
+  (quality-gates
+    (block-on-failing-tests #t)
+    (block-on-linter-errors #t)
+    (block-on-security-issues #t)
+    (require-test-coverage 80))
+
+  (zig-analysis
+    (run-zig-test #t)
+    (check-memory-leaks #t)
+    (verify-abi-exports #t)
+    (check-alignment #t)
+    (verify-block-formats #t))
+
+  (factor-analysis
+    (check-syntax #t)
+    (verify-ffi-signatures #t)
+    (check-for-stubs #t))
+
+  (forth-analysis
+    (verify-stack-effects #t)
+    (check-block-layout #t)
+    (verify-crc-implementation #t))
+
+  (security-checks
+    (scan-for-secrets #t)
+    (check-for-unsafe-operations #t)
+    (verify-input-validation #t)
+    (check-buffer-bounds #t))
+
+  (automated-fixes
+    (auto-format-code #f)
+    (auto-fix-lints #f)
+    (suggest-improvements #t))
+
+  (reporting
+    (post-pr-comments #t)
+    (generate-quality-report #t)
+    (track-quality-trends #t)))

lithoglyph/.bot_directives/echidnabot.scm

@@ -0,0 +1,39 @@
+;; SPDX-License-Identifier: PMPL-1.0-or-later
+;; Rhodibot Directives - Git Operations Automation
+;;
+;; Rhodibot handles automated git operations, commit standardization,
+;; and repository health maintenance for Lithoglyph.
+
+(rhodibot-config
+  (repo-name "lithoglyph")
+  (primary-language "zig")
+  (additional-languages "factor" "forth" "elixir")
+
+  (commit-standards
+    (format "conventional-commits")
+    (scopes "core-zig" "core-factor" "core-forth" "api" "docs" "tests")
+    (require-co-author #t)
+    (co-author "Claude Sonnet 4.5 <noreply@anthropic.com>")
+    (sign-commits #f))
+
+  (branch-protection
+    (main-branch "main")
+    (require-reviews 1)
+    (require-tests-pass #t)
+    (allow-force-push #f))
+
+  (automated-tasks
+    (auto-rebase #f)
+    (auto-merge-dependabot #f)
+    (auto-tag-releases #t)
+    (sync-forks #t))
+
+  (monitoring
+    (check-for-drift #t)
+    (verify-ci-status #t)
+    (alert-on-failed-builds #t))
+
+  (cleanup-rules
+    (delete-merged-branches #t)
+    (squash-on-merge #f)
+    (update-changelog #t)))

lithoglyph/.bot_directives/rhodibot.scm

@@ -0,0 +1,173 @@
+# CLAUDE.md - AI Assistant Instructions for Lithoglyph
+
+## Project Overview
+
+Lithoglyph (formerly "Lith") is a narrative-first, reversible, audit-grade database core. Every mutation is a story event with full provenance. The tagline: "The database where the database is part of the story."
+
+Multi-language stack in dependency order:
+1. **Forth** (core-forth/) — Block storage kernel, journaling, data model
+2. **Zig** (core-zig/) — C ABI bridge with WAL, 19 functions, block allocator
+3. **Zig** (ffi/zig/) — Delegation layer that forwards to core-zig
+4. **Idris2** (src/Lith/) — Dependent-type ABI proofs, memory layout verification
+5. **Factor** (core-factor/) — FQL runtime: parser, planner, executor
+6. **Lean 4** (normalizer/) — Normalization proofs, FD discovery (52 proofs)
+7. **Lean 4** (gql-dt/) — Dependently-typed Glyph Query Language
+8. **Zig + Rust** (beam/) — BEAM NIFs for Elixir/Erlang integration
+9. **Elixir** (lith-http/) — Phoenix HTTP API, control plane
+10. **Rust + Web** (studio/) — Tauri desktop GUI (mock data, early stage)
+11. **Zig** (api/) — REST + gRPC API (BROKEN — needs Zig 0.15.2 migration)
+
+Subprojects with own `.machine_readable/`: gql-dt/, glyphbase/, lith-http/
+
+## Architecture
+
+```
+svalinn (TLS) → lith-http (Elixir :4000) → BEAM NIFs → core-zig (C ABI) → core-forth (blocks)
+                                                 ↑
+                              Idris2 ABI proofs (src/Lith/) verify bridge contracts
+                              Lean 4 normalizer verifies schema correctness
+                              GQL-DT (Lean 4) verifies query correctness
+                              Factor FQL plans and executes queries
+```
+
+## Critical Invariants
+
+1. **IP Rename PENDING**: Code uses `Lith`/`Form` internally. Must rename to `Litho`/`Lithoglyph` before any public release. Keep "form" only where it literally means HTML/data forms.
+2. **Zero `believe_me`** in Idris2 ABI (`src/Lith/`). This is a HARD invariant — no exceptions.
+3. **Zero `sorry`** in Lean 4 proofs (normalizer/, gql-dt/). All proofs must be constructive.
+4. **`core-zig/src/bridge.zig`** is the WORKING implementation. `ffi/zig/` only delegates to it. Never add new functionality to `ffi/zig/` directly.
+5. **Proven library** lives at `/var/mnt/eclipse/repos/proven/` (104+ modules) — never bundle a copy.
+6. All Zig `@ptrCast`/`@alignCast`/`@intToPtr` must have `// SAFETY:` comments.
+7. **SCM files** ONLY in `.machine_readable/` — never in root directories.
+8. **Container runtime**: Podman, never Docker. Files: `Containerfile`, never `Dockerfile`.
+9. **Base images**: `cgr.dev/chainguard/wolfi-base:latest` or `cgr.dev/chainguard/static:latest`.
+
+## Machine-Readable Artefacts
+
+`.machine_readable/` contains:
+- `STATE.scm` — Current project state, component status, completion percentages
+- `META.scm` — Architecture decisions, development practices, design rationale
+- `ECOSYSTEM.scm` — Position in ecosystem, related projects
+- `AGENTIC.scm` — AI agent interaction patterns, autonomous agent designs
+- `NEUROSYM.scm` — Neurosymbolic integration (symbolic proofs + planned neural layer)
+- `PLAYBOOK.scm` — Operational runbook, build procedures, incident response
+- `HANDOVER.scm` — Legacy handover artefact (historical)
+- `ROADMAP.scm` — Unified roadmap across all lithoglyph subprojects
+
+## Language Policy
+
+### ALLOWED
+- **Forth** — Storage kernel (gforth)
+- **Zig** — Bridge, BEAM NIF, API layer
+- **Idris2** — ABI proofs (dependent types)
+- **Lean 4** — Normalization proofs, GQL-DT
+- **Factor** — FQL runtime (concatenative)
+- **Elixir** — OTP control plane, HTTP API
+- **Rust** — BEAM NIF (Rustler), studio backend
+- **ReScript** — Client libraries (if needed)
+- **Nickel** — Configuration
+
+### BANNED
+- TypeScript, Python, Go, Java, Node.js, npm
+
+## Build Commands
+
+### Core Components (dependency order)
+```bash
+# 1. Forth kernel (17 tests)
+cd core-forth && gforth test/lithoglyph-tests.fs
+
+# 2. Zig bridge (primary — all tests)
+cd core-zig && zig build test
+
+# 3. Zig FFI delegation (delegates to core-zig)
+cd ffi/zig && zig build test
+
+# 4. Idris2 ABI type-check (3 files, must be clean)
+idris2 --source-dir src --check src/Lith/LithBridge.idr
+idris2 --source-dir src --check src/Lith/LithLayout.idr
+idris2 --source-dir src --check src/Lith/LithForeign.idr
+
+# 5. Lean 4 normalizer (52 proofs)
+cd normalizer && lake build
+
+# 6. Factor runtime
+cd core-factor && factor -run=listener  # manual verification
+```
+
+### Satellites
+```bash
+# BEAM NIF (Rust — 0 warnings required)
+cd beam/native_rust && cargo build
+
+# BEAM NIF (Zig)
+cd beam/native && zig build
+
+# Elixir HTTP (lith-http)
+cd lith-http && mix deps.get && mix compile && mix test
+
+# GQL-DT (Lean 4)
+cd gql-dt && lake build
+
+# Studio (Tauri — mostly mock data)
+cd studio && cargo build
+```
+
+### Quick Verification
+```bash
+just test      # core-zig + ffi/zig + core-forth
+just build-all # everything in dependency order
+```
+
+## Component Status
+
+| Component | Build | Tests | Notes |
+|-----------|-------|-------|-------|
+| core-forth | PASS | 17/17 | Block storage, journal, data model |
+| core-zig | PASS | PASS | 19 real functions, WAL commit |
+| ffi/zig | PASS | PASS | Delegates to core-zig |
+| Idris2 ABI | PASS | N/A | 3 files type-check clean, 0 believe_me |
+| Lean 4 normalizer | PASS | 52 PASS | FD discovery proofs |
+| core-factor | PASS | N/A | FQL parser/planner/executor |
+| BEAM NIF (Zig) | PASS | N/A | Real FFI calls |
+| BEAM NIF (Rust) | PASS | N/A | Rustler 0.35, 0 warnings |
+| lith-http | PASS | PASS | M15 complete |
+| gql-dt | PASS | claims 100% | Needs honest audit |
+| glyphbase | ? | ? | Needs honest audit |
+| api (Zig) | BROKEN | N/A | 83 old std.http.Server call sites |
+| studio | PASS | N/A | 11 commands return mock data |
+
+## Patterns and Anti-Patterns
+
+### Banned Patterns (CI enforced)
+- `believe_me` in Idris2 — use `%foreign prim__callbackToAnyPtr` pattern instead
+- `assert_total`, `assert_smaller`, `unsafePerformIO` in Idris2
+- `sorry` in Lean 4
+- `Admitted` in Coq (if any)
+- Zig unsafe casts without `// SAFETY:` annotation
+- SQL string concatenation — use parameterized query builders
+- Hardcoded secrets — use env vars with `${VAR:-}` defaults
+
+### Key Design Patterns
+- **Bridge delegation**: `ffi/zig/` → `core-zig/` (never reverse)
+- **ABI-first**: Idris2 proofs define the interface contract, Zig implements it
+- **Proof-verified schemas**: Lean 4 normalizer proves schema correctness
+- **Narrative provenance**: Every mutation has a story — who, what, when, why
+- **WAL-first writes**: All mutations go through Write-Ahead Log before blocks
+
+## Related Projects
+
+- **verisimdb** — Octad database sibling (shares GQL patterns)
+- **quandledb** — Knot-theoretic database sibling
+- **nqc** — Normal-form Query Compiler
+- **proven** — Formally verified safety library (SafeString, SafeJson, etc.)
+- **hypatia** — Neurosymbolic CI/CD scanner
+- **gitbot-fleet** — Bot orchestration (rhodibot, echidnabot, sustainabot)
+
+## Known Issues
+
+- **API layer**: `api/src/rest.zig` and `api/src/grpc.zig` use old `std.http.Server` API — 83 call sites need Zig 0.15.2 migration
+- **Studio**: 11 Tauri commands return mock data, not real bridge calls
+- **IP rename**: `Lith`/`Form` namespace must be renamed before public release
+- **Idris2 Nat reduction**: Proof type signatures must use concrete literals, not function-defined constants (Idris2 0.8 limitation)
+- **gql-dt/glyphbase**: Claim 100% completion — need honest audit

lithoglyph/.claude/CLAUDE.md

@@ -0,0 +1,68 @@
+# SPDX-License-Identifier: PMPL-1.0-or-later
+# https://editorconfig.org
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 2
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.adoc]
+trim_trailing_whitespace = false
+
+[*.rs]
+indent_size = 4
+
+[*.zig]
+indent_size = 4
+
+[*.ada]
+indent_size = 3
+
+[*.adb]
+indent_size = 3
+
+[*.ads]
+indent_size = 3
+
+[*.ex]
+indent_size = 2
+
+[*.exs]
+indent_size = 2
+
+[*.hs]
+indent_size = 2
+
+[*.res]
+indent_size = 2
+
+[*.resi]
+indent_size = 2
+
+[*.ncl]
+indent_size = 2
+
+[*.scm]
+indent_size = 2
+
+[*.nix]
+indent_size = 2
+
+[Justfile]
+indent_style = space
+indent_size = 4
+
+[justfile]
+indent_style = space
+indent_size = 4
+
+[Makefile]
+indent_style = tab