diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6e148b4f..3ffb5663 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [1.2.0] - 2026-03-19
 
+### Added
+
+- **`specsync generate --ai`** — AI-powered spec generation. Reads source code, sends it to an LLM, and generates specs with real content (Purpose, Public API tables, Invariants, Error Cases) instead of template stubs. Configurable via `aiCommand` and `aiTimeout` in `specsync.json`, or `SPECSYNC_AI_COMMAND` env var. Defaults to Claude CLI, works with any LLM that reads stdin and writes stdout.
+- **LOC coverage tracking** — `specsync coverage` now reports lines-of-code coverage alongside file coverage. JSON output includes `loc_coverage`, `loc_covered`, `loc_total`, and `uncovered_files` with per-file LOC counts sorted by size.
+- **Flat file module detection** — `generate` and `coverage` now detect single-file modules (e.g., `src/config.rs`) in addition to subdirectory-based modules.
+- `aiCommand` and `aiTimeout` config options in `specsync.json`.
+
 ### Changed
 
 - Rewrote README for density — every line carries new information, no filler.
+- Documented `generate --ai` workflow, AI command configuration, and LOC coverage in README and docs site.
 - Streamlined docs site pages to complement rather than duplicate the README.
 - Updated CHANGELOG with previously missing 1.1.1 and 1.1.2 entries.
 
diff --git a/README.md b/README.md
index 8061e09a..0537048c 100644
--- a/README.md
+++ b/README.md
@@ -101,6 +101,7 @@ specsync init                              # Create specsync.json config
 specsync check                             # Validate specs against code
 specsync coverage                          # Show file/module coverage
 specsync generate                          # Scaffold specs for unspecced modules
+specsync generate --ai                     # AI-powered specs (reads code, writes content)
 specsync watch                             # Re-validate on every file change
 ```
 
@@ -246,7 +247,7 @@ specsync [command] [flags]
 |---------|-------------|
 | `check` | Validate all specs against source code **(default)** |
 | `coverage` | File and module coverage report |
-| `generate` | Scaffold specs for modules missing one |
+| `generate` | Scaffold specs for modules missing one (`--ai` for AI-powered content) |
 | `init` | Create default `specsync.json` |
 | `watch` | Live validation on file changes (500ms debounce) |
 
@@ -313,7 +314,9 @@ Create `specsync.json` in your project root (or run `specsync init`):
   "requiredSections": ["Purpose", "Public API", "Invariants", "Behavioral Examples", "Error Cases", "Dependencies", "Change Log"],
   "excludeDirs": ["__tests__"],
   "excludePatterns": ["**/__tests__/**", "**/*.test.ts", "**/*.spec.ts"],
-  "sourceExtensions": []
+  "sourceExtensions": [],
+  "aiCommand": "claude -p --output-format text",
+  "aiTimeout": 120
 }
 ```
 
@@ -327,25 +330,68 @@ Create `specsync.json` in your project root (or run `specsync init`):
 | `excludeDirs` | `string[]` | `["__tests__"]` | Directories excluded from coverage |
 | `excludePatterns` | `string[]` | Common test globs | File patterns excluded from coverage |
 | `sourceExtensions` | `string[]` | All supported | Restrict to specific extensions (e.g., `["ts", "rs"]`) |
+| `aiCommand` | `string?` | `claude -p ...` | Command for `generate --ai` (reads stdin prompt, writes stdout markdown) |
+| `aiTimeout` | `number?` | `120` | Seconds before AI command times out per module |
 
 ---
 
-## For AI Agents
+## Spec Generation
 
-- **`--json`** outputs structured results, no color codes to strip
-- **Exit code 1** = needs fixing; **0** = all clear
-- **`specsync generate`** bootstraps specs for existing codebases
-- **Spec files are plain markdown** — any LLM can read and write them
-- **Public API tables** use backtick-quoted names, unambiguous to parse
+`specsync generate` scans your source directories, finds modules without spec files, and scaffolds `*.spec.md` files for each one.
 
-### JSON shapes
+```bash
+specsync generate                         # Scaffold template specs for all unspecced modules
+specsync generate --ai                    # Use AI to generate filled-in specs from source code
+specsync coverage                         # See what's still missing
+```
+
+### Template mode (default)
+
+Uses your custom template (`specs/_template.spec.md`) or the built-in default. Generates frontmatter + stubbed sections with TODOs.
+
+### AI mode (`--ai`)
+
+Reads your source code, sends it to an LLM, and generates specs with real content — Purpose, Public API tables, Invariants, Error Cases, all filled in from the code. No manual filling required.
+
+The AI command is resolved in order:
+1. `"aiCommand"` in `specsync.json`
+2. `SPECSYNC_AI_COMMAND` environment variable
+3. `claude -p --output-format text` (default, requires [Claude CLI](https://docs.anthropic.com/en/docs/claude-code))
+
+Any command that reads a prompt from stdin and writes markdown to stdout works:
+
+```json
+{ "aiCommand": "claude -p --output-format text" }
+{ "aiCommand": "ollama run llama3" }
+```
+
+Set `"aiTimeout"` in `specsync.json` to control per-module timeout (default: 120 seconds).
+
+### Designed for AI agents
+
+The generate command is the entry point for LLM-powered spec workflows:
+
+```bash
+specsync generate --ai                             # AI writes specs from source code
+specsync check --json                              # validate, get structured feedback
+# LLM fixes errors from JSON output                # iterate until clean
+specsync check --strict --require-coverage 100     # enforce full coverage in CI
+```
+
+Every output format is designed for machine consumption:
+- **`--json`** on any command → structured JSON, no ANSI codes
+- **Exit code 0/1** → pass/fail, no parsing needed
+- **Spec files are plain markdown** → any LLM can read and write them
+- **Public API tables** use backtick-quoted names → unambiguous to extract
+
+### JSON output shapes
 
 ```json
 // specsync check --json
 { "passed": false, "errors": ["..."], "warnings": ["..."], "specs_checked": 12 }
 
 // specsync coverage --json
-{ "file_coverage": 85.33, "files_covered": 23, "files_total": 27, "modules": [{"name": "helpers", "has_spec": false}] }
+{ "file_coverage": 85.33, "files_covered": 23, "files_total": 27, "loc_coverage": 79.12, "loc_covered": 4200, "loc_total": 5308, "modules": [...] }
 ```
 
 ---
@@ -355,6 +401,7 @@ Create `specsync.json` in your project root (or run `specsync init`):
 ```
 src/
 ├── main.rs            CLI entry + output formatting
+├── ai.rs              AI-powered spec generation (prompt builder + command runner)
 ├── types.rs           Data types + config schema
 ├── config.rs          specsync.json loading
 ├── parser.rs          Frontmatter + spec body parsing
diff --git a/docs/_config.yml b/docs/_config.yml
index 4ae37c6e..6704c9ba 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -5,7 +5,7 @@ baseurl: "/spec-sync"
 
 remote_theme: just-the-docs/just-the-docs@v0.10.0
 
-color_scheme: dark
+color_scheme: rust
 
 aux_links:
   "GitHub":
diff --git a/docs/_sass/color_schemes/rust.scss b/docs/_sass/color_schemes/rust.scss
new file mode 100644
index 00000000..1790ab0b
--- /dev/null
+++ b/docs/_sass/color_schemes/rust.scss
@@ -0,0 +1,30 @@
+// Rust-themed dark color scheme for SpecSync docs
+// Based on just-the-docs dark scheme with orange/rust accents
+
+$body-background-color: #1e1e1e;
+$sidebar-color: #171717;
+$body-text-color: #e0e0e0;
+$body-heading-color: #f0f0f0;
+
+// Rust orange accent colors
+$link-color: #e87d2f;
+$btn-primary-color: #e87d2f;
+$feedback-color: darken($link-color, 3%);
+
+// Code blocks
+$code-background-color: #2a2a2a;
+$code-linenumber-color: #6e7681;
+$border-color: #3d3d3d;
+
+// Search
+$search-background-color: #2a2a2a;
+$search-result-preview-color: #b0b0b0;
+
+// Tables
+$table-background-color: #252525;
+
+// Navigation
+$nav-child-link-color: #c0c0c0;
+
+// Footer
+$footer-background-color: #171717;
diff --git a/docs/ai-agents.md b/docs/ai-agents.md
index bf3b425d..a466d4c5 100644
--- a/docs/ai-agents.md
+++ b/docs/ai-agents.md
@@ -7,7 +7,7 @@ nav_order: 6
 # For AI Agents
 {: .no_toc }
 
-SpecSync is built to work well with LLM-powered coding tools.
+SpecSync is built for LLM-powered coding tools — structured output, machine-readable specs, and automated scaffolding.
 {: .fs-6 .fw-300 }
 
 <details open markdown="block">
@@ -19,30 +19,85 @@ SpecSync is built to work well with LLM-powered coding tools.
 
 ---
 
-## Why It Works
+## AI-Powered Generation (`--ai`)
 
-- Specs are plain markdown — any LLM can read and write them
-- `--json` outputs structured data, no terminal color codes
-- Exit code 1 = needs fixing, 0 = all clear
-- `specsync generate` bootstraps specs for existing codebases
-- Public API tables use backtick-quoted names, unambiguous to parse
+`specsync generate --ai` reads your source code, sends it to an LLM, and generates specs with real content — not just templates with TODOs. Purpose, Public API tables, Invariants, Error Cases — all filled in from the code.
+
+```bash
+specsync generate --ai
+#   Generating specs/auth/auth.spec.md with AI...
+#     │ ---
+#     │ module: auth
+#     │ ...
+#   ✓ Generated specs/auth/auth.spec.md (3 files)
+```
+
+### Configuring the AI command
+
+The AI command is resolved in order:
+1. `"aiCommand"` in `specsync.json`
+2. `SPECSYNC_AI_COMMAND` environment variable
+3. `claude -p --output-format text` (default, requires Claude CLI)
+
+Any command that reads a prompt from stdin and writes markdown to stdout works:
+
+```json
+{
+  "aiCommand": "claude -p --output-format text",
+  "aiTimeout": 300
+}
+```
+
+```json
+{
+  "aiCommand": "ollama run llama3",
+  "aiTimeout": 60
+}
+```
+
+If AI generation fails for a module, it falls back to template generation automatically.
+
+### Template mode (no `--ai`)
+
+Without `--ai`, `specsync generate` scaffolds template specs — frontmatter populated, required sections stubbed with TODOs. Place `_template.spec.md` in your specs directory to control the generated structure.
 
 ---
 
-## Workflow
+## End-to-End Workflow
 
 ```bash
-specsync check --json                       # 1. assess current state
-# fix errors in specs or source             # 2. resolve issues
-specsync generate                           # 3. scaffold missing specs
-specsync check --strict --require-coverage 100  # 4. verify
+# One command: AI reads code, writes specs
+specsync generate --ai
+
+# Validate the generated specs against code
+specsync check --json
+
+# LLM fixes errors from JSON output, iterates until clean
+
+# CI gate with full coverage
+specsync check --strict --require-coverage 100
 ```
 
+Each step produces machine-readable output. No human in the loop required (though humans can review at any step).
+
 ---
 
-## JSON Shapes
+## Why SpecSync Works for LLMs
 
-### Check
+| Feature | Why it matters |
+|---------|---------------|
+| Plain markdown specs | Any LLM can read and write them — no custom format to learn |
+| `--json` flag on every command | Structured output, no ANSI codes to strip |
+| Exit code 0/1 | Pass/fail without parsing |
+| Backtick-quoted names in API tables | Unambiguous extraction — first backtick-quoted string per row |
+| `specsync generate` | Bootstrap from zero — LLM fills in content, not boilerplate |
+| Deterministic validation | Same input → same output, no flaky checks |
+
+---
+
+## JSON Output Shapes
+
+### `specsync check --json`
 
 ```json
 {
@@ -53,29 +108,35 @@ specsync check --strict --require-coverage 100  # 4. verify
 }
 ```
 
-- **Errors**: spec references something that doesn't exist in code — must fix
+- **Errors**: spec references something missing from code — must fix
 - **Warnings**: code exports something the spec doesn't mention — informational
 - **`--strict`**: promotes warnings to errors
 
-### Coverage
+### `specsync coverage --json`
 
 ```json
 {
   "file_coverage": 85.33,
   "files_covered": 23,
   "files_total": 27,
-  "modules": [{ "name": "helpers", "has_spec": false }]
+  "loc_coverage": 79.12,
+  "loc_covered": 4200,
+  "loc_total": 5308,
+  "modules": [{ "name": "helpers", "has_spec": false }],
+  "uncovered_files": [{ "file": "src/helpers/utils.ts", "loc": 340 }]
 }
 ```
 
+Use `modules` with `has_spec: false` to identify what `generate` would scaffold. `uncovered_files` shows LOC per uncovered file, sorted by size — prioritize the largest gaps.
+
 ---
 
 ## Writing Specs Programmatically
 
 1. Frontmatter requires `module`, `version`, `status`, `files`
-2. Status: `draft`, `review`, `stable`, `deprecated`
-3. Files: non-empty list, paths relative to project root
-4. Public API tables: backtick-quoted names in first column
+2. Status values: `draft`, `review`, `stable`, `deprecated`
+3. `files` must be non-empty, paths relative to project root
+4. Public API tables: first backtick-quoted string per row is the export name
 5. Default required sections: Purpose, Public API, Invariants, Behavioral Examples, Error Cases, Dependencies, Change Log
 
 ### Minimal valid spec
@@ -121,9 +182,13 @@ None
 
 ---
 
-## Integration Ideas
+## Integration Patterns
 
-- **Pre-commit hook**: `specsync check --strict`
-- **PR review bot**: parse `specsync check --json` output, post as PR comment
-- **Spec generation**: run `specsync generate` after adding modules
-- **AI code review**: feed JSON output to an LLM for spec update suggestions
+| Pattern | Command | How |
+|---------|---------|-----|
+| **Pre-commit hook** | `specsync check --strict` | Block commits with spec errors |
+| **PR review bot** | `specsync check --json` | Parse output, post as PR comment |
+| **Bootstrap coverage** | `specsync generate --ai` | AI writes specs from source code |
+| **Template scaffold** | `specsync generate` | Scaffold templates after adding new modules |
+| **AI code review** | `specsync check --json` | Feed errors to LLM for spec updates |
+| **Coverage gate** | `specsync check --strict --require-coverage 100` | CI enforces full coverage |
diff --git a/docs/architecture.md b/docs/architecture.md
index cf60becd..5f5557a4 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -24,6 +24,7 @@ How SpecSync is built. Useful for contributors and anyone adding language suppor
 ```
 src/
 ├── main.rs              CLI entry point (clap) + output formatting
+├── ai.rs                AI-powered spec generation (prompt builder + command runner)
 ├── types.rs             Core data types + config schema
 ├── config.rs            specsync.json loading
 ├── parser.rs            Frontmatter + spec body parsing
diff --git a/docs/cli.md b/docs/cli.md
index a386b408..7e584ec8 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -58,9 +58,12 @@ specsync coverage --json
 Scaffold spec files for modules that don't have one. Uses `specs/_template.spec.md` if present.
 
 ```bash
-specsync generate
+specsync generate                       # template mode — stubs with TODOs
+specsync generate --ai                  # AI mode — reads code, writes real content
 ```
 
+With `--ai`, source code is piped to an LLM which generates filled-in specs (Purpose, Public API tables, Invariants, etc.). The AI command is resolved from: `aiCommand` in config → `SPECSYNC_AI_COMMAND` env var → `claude -p --output-format text`. See [Configuration](configuration) for `aiCommand` and `aiTimeout`.
+
 ### `init`
 
 Create a default `specsync.json` in the current directory.
@@ -86,6 +89,7 @@ specsync watch
 | `--strict` | Warnings become errors. Recommended for CI. |
 | `--require-coverage N` | Fail if file coverage < N%. |
 | `--root <path>` | Project root directory (default: cwd). |
+| `--ai` | Use AI to generate filled-in specs instead of templates (with `generate`). |
 | `--json` | Structured JSON output, no color codes. |
 
 ---
@@ -119,6 +123,10 @@ specsync watch
   "file_coverage": 85.33,
   "files_covered": 23,
   "files_total": 27,
-  "modules": [{ "name": "helpers", "has_spec": false }]
+  "loc_coverage": 79.12,
+  "loc_covered": 4200,
+  "loc_total": 5308,
+  "modules": [{ "name": "helpers", "has_spec": false }],
+  "uncovered_files": [{ "file": "src/helpers/utils.ts", "loc": 340 }]
 }
 ```
diff --git a/docs/configuration.md b/docs/configuration.md
index c60cea3e..3ded63ca 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -40,7 +40,9 @@ Creates `specsync.json` with defaults. SpecSync also works without a config file
   "requiredSections": ["Purpose", "Public API", "Invariants", "Behavioral Examples", "Error Cases", "Dependencies", "Change Log"],
   "excludeDirs": ["__tests__"],
   "excludePatterns": ["**/__tests__/**", "**/*.test.ts", "**/*.spec.ts"],
-  "sourceExtensions": []
+  "sourceExtensions": [],
+  "aiCommand": "claude -p --output-format text",
+  "aiTimeout": 120
 }
 ```
 
@@ -58,6 +60,8 @@ Creates `specsync.json` with defaults. SpecSync also works without a config file
 | `excludeDirs` | `string[]` | `["__tests__"]` | Directory names skipped during coverage scanning |
 | `excludePatterns` | `string[]` | Common test globs | File patterns excluded from coverage (additive with language-specific test exclusions) |
 | `sourceExtensions` | `string[]` | All supported | Restrict to specific extensions (e.g., `["ts", "rs"]`) |
+| `aiCommand` | `string?` | `claude -p ...` | Command for `generate --ai` (reads stdin prompt, writes stdout markdown) |
+| `aiTimeout` | `number?` | `120` | Seconds before AI command times out per module |
 
 ---
 
diff --git a/docs/index.md b/docs/index.md
index 0f1a0a45..16d2ab9b 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -37,6 +37,7 @@ specsync init                   # create specsync.json
 specsync check                  # validate specs against code
 specsync coverage               # see what's covered
 specsync generate               # scaffold specs for unspecced modules
+specsync generate --ai          # AI-powered specs (reads code, writes content)
 specsync watch                  # re-validate on file changes
 ```