fix: Update content for Bell Labs structure consistency

Critical fixes for staging site quality:

1. Homepage (docs/pages/index.md)
   - Fixed 5 broken links from old structure
   - /canonical/* → /foundations/*
   - /tools/* → /systems/*
   - /innovations/* → /systems/*

2. Research routing (src/sif_web/routes/pages.py)
   - Added subdirectory search for research papers
   - Papers in agent-infrastructure/, information-architecture/, standards/ now accessible
   - Maintains backwards compatibility with flat structure

3. Dead code removal (src/sif_web/routes/pages.py)
   - Removed /innovations routes (lines 400-440)
   - Fixed /founders-letter to point to foundations/

4. About page (docs/pages/about.md)
   - Fixed broken /canonical link
   - Updated to reference both /manifesto and /foundations

5. Systems README (docs/systems/README.md)
   - Updated title: "SIL Tools" → "SIL Systems"
   - Removed broken /innovations links
   - Added comprehensive system listings
   - Fixed internal links to /systems/*

All changes maintain backwards compatibility via 301 redirects.
No breaking changes for users.

Author: Scott Senkeresty

docs/pages/about.md

@@ -139,7 +139,8 @@ If an agent contributes insight, structure, or decomposition, that provenance ge
 **Read our research:**
 - [Essays](/essays) — technical essays on semantic infrastructure
 - [Research](/research) — deep technical papers
-- [Canonical Documents](/canonical) — manifesto, principles, charter
+- [Manifesto](/manifesto) — YOLO and soul documents
+- [Foundations](/foundations) — principles, architecture, charter
 
 **Collaborate:**
 - [Contact us](/contact) for research collaboration

docs/pages/index.md

@@ -25,13 +25,13 @@ SIL develops **semantic infrastructure**—a substrate where:
 - **Reasoning is inspectable** — you can see how conclusions were reached
 - **Composition works** — systems combine correctly across domains
 
-This is the [Semantic Operating System](/canonical/semantic-os-architecture): persistent memory, unified representations, deterministic engines, multi-agent orchestration, and interfaces where every cognitive layer remains visible.
+This is the [Semantic Operating System](/foundations/semantic-os-architecture): persistent memory, unified representations, deterministic engines, multi-agent orchestration, and interfaces where every cognitive layer remains visible.
 
 ## Production Systems
 
 These aren't demos. They're working infrastructure proving the architecture:
 
-### [Reveal](/tools/reveal) — Progressive Code Exploration
+### [Reveal](/systems/reveal) — Progressive Code Exploration
 `pip install reveal-cli` · v0.23.1 · 2K+ downloads/month
 
 Structure-first code exploration with 10-150x token reduction. See file structure before reading content. Extract specific functions without loading entire files.
@@ -42,12 +42,12 @@ reveal app.py          # File structure (functions, classes)
 reveal app.py main     # Extract specific function
 ```
 
-### [Morphogen](/innovations/morphogen) — Cross-Domain Computation
+### [Morphogen](/systems/morphogen) — Cross-Domain Computation
 v0.11 · 1,600+ tests · 85% coverage
 
 Unified computational substrate spanning 40+ domains. MLIR-based deterministic execution with cryptographic provenance.
 
-### [GenesisGraph](/innovations/genesisgraph) — Verifiable Provenance
+### [GenesisGraph](/systems/genesisgraph) — Verifiable Provenance
 v0.3.0 · Cryptographic audit trails
 
 Every transformation produces a provenance record. Selective disclosure lets you verify without revealing everything.
@@ -80,7 +80,7 @@ SIL is the research division of the [Semantic Infrastructure Foundation](https:/
 
 - **Use the tools:** `pip install reveal-cli` and try progressive disclosure
 - **Read the research:** [Essays](/essays) and [Research Papers](/research)
-- **Explore the architecture:** [Canonical Documents](/canonical)
+- **Explore the architecture:** [Foundations](/foundations)
 - **Collaborate:** [Contact us](/contact) or visit [GitHub](https://github.com/Semantic-Infrastructure-Lab)
 
 ---

docs/systems/README.md

@@ -1,6 +1,6 @@
-# SIL Tools - Stop Wasting Money on Agent Loops
+# SIL Systems
 
-Production-ready tools demonstrating SIL principles. Use them today.
+Production-ready systems demonstrating SIL principles. Use them today.
 
 ## The Problem
 
@@ -11,9 +11,9 @@ AI agents waste billions of tokens (and dollars) on inefficient exploration patt
 
 **Global impact:** Estimated $110M+ wasted annually on preventable agent inefficiency.
 
-## Our Solution: Agent-Native Tools
+## Our Solution: Agent-Native Systems
 
-Tools designed for agents from day one, with:
+Systems designed for agents from day one, with:
 - **Progressive disclosure** - Structure before detail (10x token reduction)
 - **Strategic guidance** - When to use this vs alternatives
 - **Composable design** - Pipes, JSON output, unix philosophy
@@ -26,20 +26,6 @@ Tools designed for agents from day one, with:
 
 ---
 
-## Tools → Innovations Mapping
-
-Some tools implement specific SIL innovations:
-
-- **Reveal** → Implements [Progressive Disclosure](/innovations/progressive-disclosure) innovation
-- **Beth** (TIA integrated) → Knowledge graph + PageRank for documentation
-- **TIA** → Application workspace applying multiple SIL innovations
-
-Some tools are applications (not innovations themselves) that demonstrate SIL principles in production.
-
-**See also:** [Innovations](/innovations) for innovation descriptions and the inverse mapping
-
----
-
 ## reveal - Semantic Code Explorer ⭐
 
 **The simplest way to understand code.** Point it at a directory, file, or function. Get exactly what you need.
@@ -79,19 +65,54 @@ This pattern will extend across all SIL systems:
 - Provenance chains (GenesisGraph)
 - Multi-agent reasoning (Agent Ether)
 
-**[→ Learn more about Reveal](/tools/reveal)** | **[Try it now](https://pypi.org/project/reveal-cli/)**
+**[→ Full Reveal documentation](/systems/reveal)** | **[Try it now](https://pypi.org/project/reveal-cli/)**
 
 ---
 
-## More Tools Coming Soon
+## More Systems
+
+### Morphogen — Cross-Domain Computation
+**Status:** v0.11 | 1,600+ tests | 85% coverage
+
+Unified computational substrate spanning 40+ domains (audio, physics, circuits, CAD). MLIR-based deterministic execution with cryptographic provenance.
+
+**[→ Learn more](/systems/morphogen)**
+
+---
+
+### TiaCAD — Declarative Parametric CAD
+**Status:** ✅ Production v3.1.2 | [GitHub](https://github.com/Semantic-Infrastructure-Lab/tiacad)
+
+Parametric CAD in YAML. Semantic constraints, not just geometry. Proof that semantic infrastructure works for physical design.
+
+**[→ Learn more](/systems/tiacad)**
+
+---
+
+### GenesisGraph — Verifiable Provenance
+**Status:** ✅ Production v0.3.0 | [GitHub](https://github.com/Semantic-Infrastructure-Lab/genesisgraph)
+
+Cryptographic provenance for every transformation. Selective disclosure lets you verify without revealing everything.
+
+**[→ Learn more](/systems/genesisgraph)**
+
+---
+
+### Beth — Semantic Documentation Search
+**Status:** Integrated with TIA
+
+Knowledge graph + PageRank for documentation discovery. Semantic search with relevance ranking.
+
+**[→ Learn more](/systems/beth)**
+
+---
 
-As SIL projects mature, more production tools will be featured here:
+### Pantheon — Universal Semantic IR
+**Status:** Active research
 
-- **morphogen** - Cross-domain computation (audio, physics, circuits) - *active development*
-- **tiacad** - Declarative parametric CAD in YAML - [Production v3.1.2](https://github.com/Semantic-Infrastructure-Lab/tiacad)
-- **genesisgraph** - Verifiable process provenance - [Production v0.3.0](https://github.com/Semantic-Infrastructure-Lab/genesisgraph)
+Universal Semantic Intermediate Representation (USIR) for cross-domain semantic operations.
 
-See all **[Innovations →](/innovations)**
+**[→ Learn more](/systems/pantheon)**
 
 ---
 

src/sif_web/routes/pages.py

@@ -331,11 +331,23 @@ async def research(request: Request) -> Response:
 
     @router.get("/research/{name}", response_class=HTMLResponse)
     async def research_paper(request: Request, name: str) -> Response:
-        """Individual research paper."""
+        """Individual research paper - handles both flat and subdirectory structure."""
         # Map URL name to filename
         filename = name.upper().replace("-", "_") + ".md"
+
+        # Try root level first
         paper_path = Path("docs/research") / filename
 
+        # If not found, search in subdirectories
+        if not paper_path.exists():
+            research_dir = Path("docs/research")
+            for subdir in research_dir.iterdir():
+                if subdir.is_dir():
+                    candidate = subdir / filename
+                    if candidate.exists():
+                        paper_path = candidate
+                        break
+
         if not paper_path.exists():
             raise HTTPException(status_code=404, detail=f"Research paper not found: {name}")
 
@@ -393,52 +405,6 @@ async def canonical_doc_redirect(request: Request, name: str) -> Response:
         else:
             return RedirectResponse(url=f"/foundations/{name}", status_code=301)
 
-    # =========================================================================
-    # End Routes
-    # =========================================================================
-
-    @router.get("/innovations", response_class=HTMLResponse)
-    async def innovations_index(request: Request) -> Response:
-        """Innovations index - Major projects and systems."""
-        return render_markdown_page(
-            request,
-            Path("docs/innovations/README.md"),
-            "Innovations - Semantic Infrastructure Lab",
-            "/innovations",
-        )
-
-    @router.get("/innovations/{name}", response_class=HTMLResponse)
-    async def innovation_page(request: Request, name: str) -> Response:
-        """Individual innovation/project page."""
-        # Map URL name to filename
-        filename = name.upper().replace("-", "_") + ".md"
-        doc_path = Path("docs/innovations") / filename
-
-        if not doc_path.exists():
-            raise HTTPException(status_code=404, detail=f"Innovation not found: {name}")
-
-        content = doc_path.read_text()
-
-        # Extract title from first H1
-        title = f"{name.replace('-', ' ').title()} - SIL"
-        for line in content.split("\n"):
-            if line.startswith("# "):
-                title = line[2:].strip() + " - SIL"
-                break
-
-        html_content = markdown_renderer.render(content)
-
-        return templates.TemplateResponse(
-            "page.html",
-            {
-                "request": request,
-                "title": title,
-                "content": html_content,
-                "nav_items": nav_items,
-                "current_page": "/innovations",
-            },
-        )
-
     # =========================================================================
     # Founder's Letter (Legacy URL support)
     # =========================================================================
@@ -448,7 +414,7 @@ async def founders_letter(request: Request) -> Response:
         """Founder's Letter - direct access."""
         return render_markdown_page(
             request,
-            Path("docs/canonical/FOUNDERS_LETTER.md"),
+            Path("docs/foundations/FOUNDERS_LETTER.md"),
             "Founder's Letter - Semantic Infrastructure Lab",
             "/",
         )