docs: Overhaul AGENTS.md, update README, add pipeline spec and Phase B plan

AGENTS.md: Comprehensive rewrite adding file deletion safeguards,
destructive git command protocol, Rust toolchain conventions, code
editing discipline rules, compiler check requirements, TDD mandate,
MCP Agent Mail coordination protocol, beads/bv/ubs/ast-grep/cass
tool documentation, and session completion workflow.

README.md: Document NO_COLOR/CLICOLOR env vars, --since 1m duration,
project resolution cascading match logic, lore health and robot-docs
commands, exit codes 17 (not found) and 18 (ambiguous match),
--color/--quiet global flags, dirty_sources and
pending_discussion_fetches tables, and version command git hash output.

docs/embedding-pipeline-hardening.md: Detailed spec covering the three
problems from the chunk size reduction (broken --full wiring, mixed
chunk sizes in vector space, static dedup multiplier) with decision
records, implementation plan, and acceptance criteria.

docs/phase-b-temporal-intelligence.md: Draft planning document for
transforming gitlore from a search engine into a temporal code
intelligence system by ingesting structured event data from GitLab.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

README.md

@@ -140,6 +140,8 @@ Create a personal access token with `read_api` scope:
 | `LORE_ROBOT` | Enable robot mode globally (set to `true` or `1`) | No |
 | `XDG_CONFIG_HOME` | XDG Base Directory for config (fallback: `~/.config`) | No |
 | `XDG_DATA_HOME` | XDG Base Directory for data (fallback: `~/.local/share`) | No |
+| `NO_COLOR` | Disable color output when set (any value) | No |
+| `CLICOLOR` | Standard color control (0 to disable) | No |
 | `RUST_LOG` | Logging level filter (e.g., `lore=debug`) | No |
 
 ## Commands
@@ -162,6 +164,7 @@ lore issues -l bug -l urgent          # Multiple labels
 lore issues -m "v1.0"                 # By milestone title
 lore issues --since 7d               # Updated in last 7 days
 lore issues --since 2w               # Updated in last 2 weeks
+lore issues --since 1m               # Updated in last month
 lore issues --since 2024-01-01       # Updated since date
 lore issues --due-before 2024-12-31  # Due before date
 lore issues --has-due                 # Only issues with due dates
@@ -174,6 +177,17 @@ When listing, output includes: IID, title, state, author, assignee, labels, and
 
 When showing a single issue (e.g., `lore issues 123`), output includes: title, description, state, author, assignees, labels, milestone, due date, web URL, and threaded discussions.
 
+#### Project Resolution
+
+The `-p` / `--project` flag uses cascading match logic across all commands:
+
+1. **Exact match**: `group/project`
+2. **Case-insensitive**: `Group/Project`
+3. **Suffix match**: `project` matches `group/project` (if unambiguous)
+4. **Substring match**: `typescript` matches `vs/typescript-code` (if unambiguous)
+
+If multiple projects match, an error lists the candidates with a hint to use the full path.
+
 ### `lore mrs`
 
 Query merge requests from local database, or show a specific MR.
@@ -221,14 +235,14 @@ lore search "deploy" --author username        # Filter by author
 lore search "deploy" -p group/repo           # Filter by project
 lore search "deploy" --label backend          # Filter by label (AND logic)
 lore search "deploy" --path src/             # Filter by file path (trailing / for prefix)
-lore search "deploy" --after 7d              # Created after (7d, 2w, or YYYY-MM-DD)
+lore search "deploy" --after 7d              # Created after (7d, 2w, 1m, or YYYY-MM-DD)
 lore search "deploy" --updated-after 2w      # Updated after
 lore search "deploy" -n 50                    # Limit results (default 20, max 100)
 lore search "deploy" --explain               # Show ranking explanation per result
 lore search "deploy" --fts-mode raw          # Raw FTS5 query syntax (advanced)
 ```
 
-Requires `lore generate-docs` (or `lore sync`) to have been run at least once. Semantic mode requires Ollama with the configured embedding model.
+Requires `lore generate-docs` (or `lore sync`) to have been run at least once. Semantic and hybrid modes require `lore embed` (or `lore sync`) to have generated vector embeddings via Ollama.
 
 ### `lore sync`
 
@@ -359,12 +373,32 @@ Run pending database migrations.
 lore migrate
 ```
 
+### `lore health`
+
+Quick pre-flight check for config, database, and schema version. Exits 0 if healthy, 1 if unhealthy.
+
+```bash
+lore health
+```
+
+Useful as a fast gate before running queries or syncs. For a more thorough check including authentication and project access, use `lore doctor`.
+
+### `lore robot-docs`
+
+Machine-readable command manifest for agent self-discovery. Returns a JSON schema of all commands, flags, exit codes, and example workflows.
+
+```bash
+lore robot-docs                   # Pretty-printed JSON
+lore --robot robot-docs           # Compact JSON for parsing
+```
+
 ### `lore version`
 
-Show version information.
+Show version information including the git commit hash.
 
 ```bash
 lore version
+# lore version 0.1.0 (abc1234)
 ```
 
 ## Robot Mode
@@ -422,6 +456,8 @@ Errors return structured JSON to stderr:
 | 14 | Ollama unavailable |
 | 15 | Ollama model not found |
 | 16 | Embedding failed |
+| 17 | Not found (entity does not exist) |
+| 18 | Ambiguous match (use `-p` to specify project) |
 | 20 | Config not found |
 
 ## Configuration Precedence
@@ -439,8 +475,13 @@ Settings are resolved in this order (highest to lowest priority):
 lore -c /path/to/config.json <command>   # Use alternate config
 lore --robot <command>                    # Machine-readable JSON
 lore -J <command>                         # JSON shorthand
+lore --color never <command>              # Disable color output
+lore --color always <command>             # Force color output
+lore -q <command>                         # Suppress non-essential output
 ```
 
+Color output respects `NO_COLOR` and `CLICOLOR` environment variables in `auto` mode (the default).
+
 ## Shell Completions
 
 Generate shell completions for tab-completion support:
@@ -480,6 +521,8 @@ Data is stored in SQLite with WAL mode and foreign keys enabled. Main tables:
 | `documents` | Extracted searchable text for FTS and embedding |
 | `documents_fts` | FTS5 full-text search index |
 | `embeddings` | Vector embeddings for semantic search |
+| `dirty_sources` | Entities needing document regeneration after ingest |
+| `pending_discussion_fetches` | Queue for discussion fetch operations |
 | `sync_runs` | Audit trail of sync operations |
 | `sync_cursors` | Cursor positions for incremental sync |
 | `app_locks` | Crash-safe single-flight lock |