docs: Update documentation for search pipeline and Phase A spec

- README.md: Add hybrid search and robot mode to feature list. Update
  quick start to use new noun-first CLI syntax (lore issues, lore mrs,
  lore search). Add embedding configuration section. Update command
  examples throughout.

- AGENTS.md: Update robot mode examples to new CLI syntax. Add search,
  sync, stats, and generate-docs commands to the robot mode reference.
  Update flag conventions (-n for limit, -s for state, -J for JSON).

- docs/prd/checkpoint-3.md: Major expansion with gated milestone
  structure (Gate A: lexical, Gate B: hybrid, Gate C: sync). Add
  prerequisite rename note, code sample conventions, chunking strategy
  details, and sqlite-vec rowid encoding scheme. Clarify that Gate A
  requires only SQLite + FTS5 with no sqlite-vec dependency.

- docs/phase-a-spec.md: New detailed specification for Gate A (lexical
  search MVP) covering document schema, FTS5 configuration, dirty
  queue mechanics, CLI interface, and acceptance criteria.

- docs/api-efficiency-findings.md: Analysis of GitLab API pagination
  behavior and efficiency observations from production sync runs.
  Documents the missing x-next-page header issue and heuristic fix.

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

AGENTS.md

@@ -33,38 +33,50 @@ The `lore` CLI has a robot mode optimized for AI agent consumption with structur
 
 ```bash
 # Explicit flag
-lore --robot list issues
+lore --robot issues -n 10
+
+# JSON shorthand (-J)
+lore -J issues -n 10
 
 # Auto-detection (when stdout is not a TTY)
-lore list issues | jq .
+lore issues | jq .
 
 # Environment variable
-LORE_ROBOT=true lore list issues
+LORE_ROBOT=1 lore issues
 ```
 
 ### Robot Mode Commands
 
 ```bash
 # List issues/MRs with JSON output
-lore --robot list issues --limit=10
-lore --robot list mrs --state=opened
+lore --robot issues -n 10
+lore --robot mrs -s opened
+
+# Show detailed entity info
+lore --robot issues 123
+lore --robot mrs 456 -p group/repo
 
 # Count entities
 lore --robot count issues
-lore --robot count discussions --type=mr
+lore --robot count discussions --for mr
 
-# Show detailed entity info
-lore --robot show issue 123
-lore --robot show mr 456 --project=group/repo
+# Search indexed documents
+lore --robot search "authentication bug"
 
 # Check sync status
-lore --robot sync-status
+lore --robot status
 
-# Run ingestion (quiet, JSON summary)
-lore --robot ingest --type=issues
+# Run full sync pipeline
+lore --robot sync
+
+# Run ingestion only
+lore --robot ingest issues
 
 # Check environment health
 lore --robot doctor
+
+# Document and index statistics
+lore --robot stats
 ```
 
 ### Response Format
@@ -102,8 +114,8 @@ Errors return structured JSON to stderr:
 
 ### Best Practices
 
-- Use `lore --robot` for all agent interactions
+- Use `lore --robot` or `lore -J` for all agent interactions
 - Check exit codes for error handling
 - Parse JSON errors from stderr
-- Use `--limit` to control response size
+- Use `-n` / `--limit` to control response size
 - TTY detection handles piped commands automatically