fix: escape LIKE wildcards in NodeQuery.fileFilter and nameLike (#446)

* feat: add Repository abstraction with InMemoryRepository for testing pyramid (3.13)

Introduce a Repository base class, InMemoryRepository (Maps-backed, no
SQLite), and SqliteRepository (delegates to existing fn(db,...) functions).
Includes fluent TestRepoBuilder fixture factory and 105 new tests
(51 unit + 54 parity) verifying behavioral equivalence between both
implementations. Existing code and tests remain unchanged.

Impact: 139 functions changed, 6 affected

* fix: address PR review feedback from Greptile

- Add kind/role validation to InMemoryRepository.findNodesForTriage
  matching SqliteRepository behavior (throws ConfigError)
- Optimize findIntraFileCallEdges sort with pre-built lookup map
  instead of spreading nodes Map per comparison
- Remove dead #nameIndex field from TestRepoBuilder
- Add validation parity tests for invalid kind/role

Impact: 5 functions changed, 0 affected

* fix: throw on duplicate node names in TestRepoBuilder.build()

Impact: 2 functions changed, 0 affected

* style: format duplicate-name error for biome line length

Impact: 2 functions changed, 0 affected

* fix: check for duplicate names before adding node to repo

Move the duplicate-name guard before repo.addNode() so the repo
is not mutated when a duplicate is detected.

Impact: 2 functions changed, 0 affected

* fix: escape LIKE special chars in InMemoryRepository file filters

findNodesByScope, findNodeByQualifiedName, findNodesWithFanIn,
listFunctionNodes, and findNodesForTriage all passed user-provided
strings directly into likeToRegex without escaping % and _ chars.
This caused divergence from SQLite which uses escapeLike + ESCAPE '\'.

Also adds parity tests for findNodesByScope, findNodeByQualifiedName,
findNodesWithFanIn, findFileNodes, findNodeChildren, import queries,
getCallableNodes, getFileNodesAll, getImportEdges, and hasCfgTables.

Impact: 7 functions changed, 5 affected

* style: format repository-parity test file

* fix: align InMemoryRepository noTests filter with SQLite excludeTests

The in-memory noTests filter only checked .test. and .spec. patterns,
missing __test__, __tests__, and .stories. that the SQLite query-builder
excludes. Add the missing patterns to both findNodesForTriage and
iterateFunctionNodes. Extend parity test fixtures with __tests__ and
.stories. nodes so the divergence is caught automatically.

Impact: 5 functions changed, 0 affected

* fix: escape LIKE wildcards in NodeQuery.fileFilter and nameLike

fileFilter() and nameLike() in query-builder.js passed user input
directly into LIKE patterns without escaping, so _ and % acted as
wildcards instead of literals. This caused a parity gap where the
SQLite findNodesWithFanIn treated _ as a wildcard but the in-memory
version (which already called escapeLike) treated it as literal.

Fix: add escapeLike() to query-builder.js (exported), use it in
fileFilter() and nameLike() with ESCAPE '\', and deduplicate the
copy in nodes.js by importing from query-builder.js.

* fix: import escapeLike from query-builder instead of duplicating it

* fix(deps): pin native binaries to 3.1.4 in optionalDependencies

Closes #454

* docs: add dogfood report for v3.1.4

Author: carlos-alm