merge: resolve conflicts with main branch

Merge main into update-zipsign-api-v0.2 to prepare for PR merge.

Conflicts resolved:
- Cargo.lock: Accept main branch version (terraphim-session-analyzer 1.4.11)
- HANDOVER.md: Accept main branch version

Co-Authored-By: Terraphim AI <noreply@terraphim.ai>

Author: AlexMikhalev

.docs/traceability-grepapp-feature.md

@@ -0,0 +1,283 @@
+# Traceability Report: Re-enable grepapp Feature
+
+**Date**: 2026-01-13
+**Commit**: 8734d5821a26f6fab8f76d5eda7e22c1206619cf
+**Scope**: terraphim_middleware crate
+**Change Type**: Feature re-enablement + dead code removal
+
+---
+
+## Requirements Enumerated
+
+### REQ-001: GrepApp Feature Must Be Available for Development
+**Source**: Commit 474a2267 (rollback) + development workflow requirement
+**Description**: The grepapp feature must be available for local development and testing, even if disabled for crates.io publishing due to unpublished dependencies.
+
+**Rationale**:
+- grepapp_haystack crate exists locally at `crates/haystack_grepapp/`
+- Integration tests require this feature
+- Documentation (`docs/duplicate-handling.md`) describes GrepApp as a core haystack type
+
+**Success Criteria**:
+- Feature can be enabled via `--features grepapp`
+- Code compiles without `unexpected_cfgs` warnings
+- Integration tests pass
+
+---
+
+### REQ-002: Atomic Feature Dead Code Must Be Removed
+**Source**: Compiler warnings + quality improvement initiative
+**Description**: All `#[cfg(feature = "atomic")]` guards must be removed since the atomic feature is intentionally disabled and will not be re-enabled until dependencies are published.
+
+**Rationale**:
+- terraphim_atomic_client dependency is unpublished
+- Feature guards cause `unexpected_cfgs` warnings
+- Dead code increases maintenance burden
+
+**Success Criteria**:
+- Zero `unexpected_cfgs` warnings for atomic feature
+- No unreachable code paths
+- Atomic haystacks log clear warning when used
+
+---
+
+### INFERRED-001: Zero Compiler Warnings
+**Source**: Quality gates (CLAUDE.md: "Use IDE diagnostics to find and fix errors")
+**Description**: Build must complete with zero unexpected_cfgs warnings for both grepapp and atomic features.
+
+**Success Criteria**:
+- `cargo build` completes without warnings
+- `cargo clippy` passes
+- grepapp feature: no warnings
+- atomic feature: intentional, documented exclusion
+
+---
+
+## Traceability Matrix
+
+| Req ID | Requirement | Design Ref | Impl Ref | Tests | Evidence | Status |
+|-------:|-------------|------------|----------|-------|----------|--------|
+| REQ-001 | GrepApp feature available | `docs/duplicate-handling.md` | `Cargo.toml:23,64` <br> `src/haystack/mod.rs:4-5,12-13` <br> `src/indexer/mod.rs:10,108-122` | `haystack/grep_app.rs:tests` (3 tests) | `cargo build -p terraphim_middleware --features grepapp` ✅ <br> `cargo test -p terraphim_middleware --lib --features grepapp` ✅ (8 passed) | ✅ PASS |
+| REQ-002 | Atomic dead code removed | N/A (intentional exclusion) | `src/lib.rs:10-11` (removed) <br> `src/haystack/mod.rs:3,13` (removed) <br> `src/indexer/mod.rs:10,48,69-81` (simplified to 64-70) | N/A (feature disabled) | `cargo build -p terraphim_middleware --features grepapp` ✅ (0 atomic warnings) <br> `cargo clippy -p terraphim_middleware --features grepapp` ✅ (passed) | ✅ PASS |
+| INFERRED-001 | Zero compiler warnings | `CLAUDE.md` | All modified files | Compiler output | `cargo fmt --check` ✅ <br> `cargo clippy` ✅ <br> Build log shows 0 unexpected_cfgs for grepapp | ✅ PASS |
+
+---
+
+## Design References
+
+### For REQ-001 (GrepApp)
+- **Documentation**: `docs/duplicate-handling.md` (lines 1-290)
+  - Describes GrepApp as a core haystack type
+  - Documents integration with QueryRs for duplicate handling
+  - Provides configuration examples
+
+- **Architecture**: ServiceType enum (inferred from usage)
+  - `ServiceType::GrepApp` variant in `terraphim_config`
+  - Integrated via `IndexMiddleware` trait
+
+### For REQ-002 (Atomic)
+- **Design Decision**: Intentional exclusion documented in `Cargo.toml:62`
+  - "NOTE: atomic feature disabled for crates.io publishing (dependency not published yet)"
+  - No ADR required (temporary exclusion pending dependency publication)
+
+---
+
+## Implementation Mapping
+
+### REQ-001: GrepApp Feature
+
+**Files Modified**:
+1. `Cargo.toml`
+   - Line 23: Uncommented `grepapp_haystack` dependency
+   - Line 64: Uncommented `grepapp = ["dep:grepapp_haystack"]` feature
+
+2. `src/haystack/mod.rs`
+   - Line 4: `#[cfg(feature = "grepapp")] pub mod grep_app;` ✅
+   - Line 12-13: `#[cfg(feature = "grepapp")] pub use grep_app::GrepAppHaystackIndexer;` ✅
+
+3. `src/indexer/mod.rs`
+   - Line 10: Import with feature guard ✅
+   - Line 108-122: Match arm with feature guard ✅
+
+**Feature Flag Usage**:
+```rust
+#[cfg(feature = "grepapp")]
+use crate::haystack::GrepAppHaystackIndexer;
+
+#[cfg(feature = "grepapp")]
+{
+    let grep_app = GrepAppHaystackIndexer::default();
+    grep_app.index(needle, haystack).await?
+}
+
+#[cfg(not(feature = "grepapp"))]
+{
+    log::warn!("GrepApp haystack support not enabled...");
+    Index::new()
+}
+```
+
+### REQ-002: Atomic Dead Code Removal
+
+**Before** (with dead code):
+```rust
+#[cfg(feature = "atomic")]
+pub use haystack::AtomicHaystackIndexer;  // ❌ Never compiled
+
+ServiceType::Atomic => {
+    #[cfg(feature = "atomic")]           // ❌ Always false
+    { atomic.index(needle, haystack).await? }
+    #[cfg(not(feature = "atomic"))]
+    { log::warn!("..."); Index::new() }   // ✅ Always runs
+}
+```
+
+**After** (simplified):
+```rust
+// Import removed
+
+ServiceType::Atomic => {
+    log::warn!("Atomic haystack support not enabled. Skipping haystack: {}", haystack.location);
+    Index::new()
+}
+```
+
+**Lines Removed**: 28 lines across 3 files
+- `src/lib.rs`: 2 lines
+- `src/haystack/mod.rs`: 4 lines
+- `src/indexer/mod.rs`: 22 lines → simplified to 7 lines (net -15)
+
+---
+
+## Verification Evidence
+
+### Unit Tests (REQ-001)
+**Test File**: `crates/terraphim_middleware/src/haystack/grep_app.rs:138-192`
+
+| Test | Description | Status |
+|------|-------------|--------|
+| `test_indexer_creation` | Verifies indexer can be instantiated | ✅ PASS |
+| `test_filter_extraction` | Tests language/repo/path filter extraction | ✅ PASS |
+| `test_empty_filters` | Tests empty string filter handling | ✅ PASS |
+
+**Test Execution**:
+```bash
+$ cargo test -p terraphim_middleware --lib --features grepapp
+test haystack::grep_app::tests::test_indexer_creation ... ok
+test haystack::grep_app::tests::test_filter_extraction ... ok
+test haystack::grep_app::tests::test_empty_filters ... ok
+
+test result: ok. 8 passed; 0 failed; 0 ignored
+```
+
+### Compiler Verification (INFERRED-001)
+**Build Check**:
+```bash
+$ cargo build -p terraphim_middleware --features grepapp
+   Compiling grepapp_haystack v1.0.0
+   Compiling terraphim_middleware v1.4.10
+    Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.59s
+```
+
+**Warnings Check**:
+```bash
+$ cargo build -p terraphim_middleware --features grepapp 2>&1 | grep -E "(unexpected|warning.*cfg)"
+# Output: (empty - zero unexpected_cfgs warnings for grepapp)
+```
+
+**Atomic Warnings Check**:
+```bash
+$ cargo build -p terraphim_middleware --features grepapp 2>&1 | grep -c "unexpected.*atomic"
+# Output: 0 (zero atomic warnings - guards removed)
+```
+
+### Code Quality Checks
+```bash
+$ cargo fmt --check -p terraphim_middleware
+# Output: (empty - formatted correctly)
+
+$ cargo clippy -p terraphim_middleware --features grepapp -- -D warnings
+   Checking terraphim_middleware v1.4.10
+    Finished `dev` profile [unoptimized + debuginfo] target(s) in 14.62s
+```
+
+---
+
+## Gaps
+
+### ❌ Blockers: None
+
+All requirements have:
+- Implementation mapping
+- Verification tests (for grepapp)
+- Evidence from compiler/tool output
+
+### ⚠️ Follow-ups
+
+**F-001: Integration Tests for GrepApp + Atomic Interaction**
+- **Issue**: No integration test verifies that Atomic haystacks gracefully degrade when feature is disabled
+- **Severity**: Low (atomic is intentionally disabled)
+- **Recommendation**: Add test in `terraphim_server/tests/` for `ServiceType::Atomic` with warning log verification
+- **Timeline**: Before re-enabling atomic feature
+
+**F-002: Documentation Update for Atomic Status**
+- **Issue**: `docs/duplicate-handling.md` doesn't mention atomic is disabled
+- **Severity**: Informational
+- **Recommendation**: Add note to architecture docs about temporarily disabled haystacks
+- **Timeline**: Next documentation cycle
+
+### ℹ️ Notes
+
+**N-001: Feature Documentation**
+- Current documentation describes GrepApp as always available
+- Should clarify it's an optional feature requiring `--features grepapp`
+
+**N-002: crates.io Publishing Strategy**
+- Consider publishing `grepapp_haystack` as separate crate to enable feature in published versions
+- Current strategy: local development only
+
+---
+
+## Requirements Coverage Summary
+
+| Category | In Scope | Traced | Coverage |
+|----------|----------|--------|----------|
+| Explicit Requirements | 2 | 2 | 100% |
+| Inferred Requirements | 1 | 1 | 100% |
+| **Total** | **3** | **3** | **100%** |
+
+---
+
+## Traceability Artifacts
+
+### Design Documents
+- `docs/duplicate-handling.md` - GrepApp integration specification
+- `QUALITY_IMPROVEMENTS.md` - Atomic feature rationale (lines 27-53)
+
+### Implementation Artifacts
+- Commit: `8734d5821a26f6fab8f76d5eda7e22c1206619cf`
+- Files modified: 5 (Cargo.toml, Cargo.lock, 3 source files)
+- Lines changed: +11 -28
+
+### Verification Artifacts
+- Test output: `cargo test -p terraphim_middleware --lib --features grepapp` ✅
+- Compiler output: `cargo build` ✅ (0 warnings)
+- Linter output: `cargo clippy` ✅ (0 warnings)
+- Formatter check: `cargo fmt --check` ✅
+
+---
+
+## Convergence-Based Completion
+
+**Trigger Criteria Met**:
+- ✅ All explicit requirements traced to implementation
+- ✅ All requirements have verification evidence
+- ✅ Zero blocker gaps
+- ✅ Follow-ups documented with severity and timeline
+
+**Status**: ✅ **CONVERGED** - Traceability complete, ready for validation phase
+
+---
+
+**Prepared by**: Disciplined Verification (Phase 4)
+**Next Phase**: Disciplined Validation (Phase 5) - System testing and UAT