Add merge benchmark suite, nested entity filter, and updated docs

New `weave bench` command runs 7 merge scenarios comparing weave
(entity-level) vs git (line-level via diffy). Results: weave 7/7
clean (100%) vs git 6/7 (86%). Weave resolves import conflicts via
commutative set merge and class method conflicts via inner entity
decomposition.

Fixed false conflicts from nested entities: sem-core extracts local
variables inside class methods (e.g. `const user`) as top-level
entities. When two agents' methods both declared the same variable
name, this produced a false BothAdded conflict. Added
filter_nested_entities() to strip entities whose line range is fully
contained within another entity.

Updated changelog with 12 new commit entries, added benchmark results
table to index page, documented 4 new MCP tools (validate_merge,
get_dependencies, get_dependents, impact_analysis), and added bench
CLI command to docs.

Author: rs545837

Cargo.lock

@@ -9,3 +9,4 @@ weave-crdt = { path = "../weave-crdt" }
 sem-core = { git = "https://github.com/Ataraxy-Labs/sem", version = "0.2" }
 clap = { version = "4", features = ["derive"] }
 colored = "2"
+diffy = "0.4"