Turns issues into links for #503

(cherry picked from commit 5d8af6a)

Author: Justin Makeig

CHANGELOG.md

@@ -3,74 +3,74 @@
 ## 4.0.0
 
 #### New Functionality
-- #400 - Optic API
-- #402 - geo double precision and geo polygon search
-- #404 - add Kerberos support
-- #413 - add support for document metadata values
-- #406 - certificate-based authentication
-- #414 - Bitemporal ML9 features - version URI, Wipe, Protect, document patch
-- #465 - Data Movement SDK
-- #466 - add StructuredQueryBuilder.coordSystem to set Geo coordinate system
-- #473 - send header "ML-Agent-ID: java" with every HTTP request so REST layer can track which calls come
+- [#400](https://github.com/marklogic/java-client-api/issues/400) - Optic API
+- [#402](https://github.com/marklogic/java-client-api/issues/402) - geo double precision and geo polygon search
+- [#404](https://github.com/marklogic/java-client-api/issues/404) - add Kerberos support
+- [#413](https://github.com/marklogic/java-client-api/issues/413) - add support for document metadata values
+- [#406](https://github.com/marklogic/java-client-api/issues/406) - certificate-based authentication
+- [#414](https://github.com/marklogic/java-client-api/issues/414) - Bitemporal ML9 features - version URI, Wipe, Protect, document patch
+- [#465](https://github.com/marklogic/java-client-api/issues/465) - Data Movement SDK
+- [#466](https://github.com/marklogic/java-client-api/issues/466) - add StructuredQueryBuilder.coordSystem to set Geo coordinate system
+- [#473](https://github.com/marklogic/java-client-api/issues/473) - send header "ML-Agent-ID: java" with every HTTP request so REST layer can track which calls come
          from Java Client API
-- #550 - add Capability NODE_UPDATE
+- [#550](https://github.com/marklogic/java-client-api/issues/550) - add Capability NODE_UPDATE
 
 #### Improvements and Bug Fixes
 - many javadoc improvements
-- #210 - fail fast when library module path doesn't begin with /ext
-- #234 - offer a way to close the input source for XMLStreamReaderHandle
-- #241 - fix misleading WARN warning message from values call
-- #249 - fixes DocumentPatchBuilder.replaceValue with numbers or booleans
-- #256 - be explicit about desired format of QBE response
-- #262 - update SearchHandle to support search:extracted elements
-- #288 - support changes made in server-generated metadata for binary docs
-- #292 - support changes made in search:search response with extracted results
-- #294 - DocumentPage.size was including metadata in counts but should not have
-- #365 - reduce duplicate code in JerseyServices
-- #421 - Some of the read handlers do not populate properly formats and mime-types when used with ResourceServices
-- #424 - remove logback dependency so slf4j works as it should
-- #436 - rename java-client-api-M.m.p.jar JAR to marklogic-client-api-M.m.p.jar
-- #448 - Efficiencies: avoid Object construction, auto-boxing, etc.
-- #486 - PojoRepository.count(query) does not scope count with the query
-- #524 - add support for markdown javadocs
-- #560 - support new 428 status code for missing content version
-- #582 - NullPointerException thrown while doing eval() with client object created with incorrect credentials
-- #610 - remove support for deprecated keyvalue endpoint
-- #621 - remove deprecated APIs
-- #651 - don't set the handle format from the descriptor if it's null
-- #687 - clean up indenting across the project## 3.0.7
+- [#210](https://github.com/marklogic/java-client-api/issues/210) - fail fast when library module path doesn't begin with /ext
+- [#234](https://github.com/marklogic/java-client-api/issues/234) - offer a way to close the input source for XMLStreamReaderHandle
+- [#241](https://github.com/marklogic/java-client-api/issues/241) - fix misleading WARN warning message from values call
+- [#249](https://github.com/marklogic/java-client-api/issues/249) - fixes DocumentPatchBuilder.replaceValue with numbers or booleans
+- [#256](https://github.com/marklogic/java-client-api/issues/256) - be explicit about desired format of QBE response
+- [#262](https://github.com/marklogic/java-client-api/issues/262) - update SearchHandle to support search:extracted elements
+- [#288](https://github.com/marklogic/java-client-api/issues/288) - support changes made in server-generated metadata for binary docs
+- [#292](https://github.com/marklogic/java-client-api/issues/292) - support changes made in search:search response with extracted results
+- [#294](https://github.com/marklogic/java-client-api/issues/294) - DocumentPage.size was including metadata in counts but should not have
+- [#365](https://github.com/marklogic/java-client-api/issues/365) - reduce duplicate code in JerseyServices
+- [#421](https://github.com/marklogic/java-client-api/issues/421) - Some of the read handlers do not populate properly formats and mime-types when used with ResourceServices
+- [#424](https://github.com/marklogic/java-client-api/issues/424) - remove logback dependency so slf4j works as it should
+- [#436](https://github.com/marklogic/java-client-api/issues/436) - rename java-client-api-M.m.p.jar JAR to marklogic-client-api-M.m.p.jar
+- [#448](https://github.com/marklogic/java-client-api/issues/448) - Efficiencies: avoid Object construction, auto-boxing, etc.
+- [#486](https://github.com/marklogic/java-client-api/issues/486) - PojoRepository.count(query) does not scope count with the query
+- [#524](https://github.com/marklogic/java-client-api/issues/524) - add support for markdown javadocs
+- [#560](https://github.com/marklogic/java-client-api/issues/560) - support new 428 status code for missing content version
+- [#582](https://github.com/marklogic/java-client-api/issues/582) - NullPointerException thrown while doing eval() with client object created with incorrect credentials
+- [#610](https://github.com/marklogic/java-client-api/issues/610) - remove support for deprecated keyvalue endpoint
+- [#621](https://github.com/marklogic/java-client-api/issues/621) - remove deprecated APIs
+- [#651](https://github.com/marklogic/java-client-api/issues/651) - don't set the handle format from the descriptor if it's null
+- [#687](https://github.com/marklogic/java-client-api/issues/687) - clean up indenting across the project## 3.0.7
 
 ### 3.0.7
 
 - some javadoc improvements and code/test cleanup
-- #423 - add support to SearchHandle for extract-resolution time
+- [#423](https://github.com/marklogic/java-client-api/issues/423) - add support to SearchHandle for extract-resolution time
 - #592, #594, #598 - chunked HTTP broke certain XML parsers unless we set XMLInputFactory.isCoalescing to true
 - full list [here](https://github.com/marklogic/java-client-api/compare/3.0.6...3.0.7)
 
 ### 3.0.6
 
 - some javadoc improvements and code/test cleanup
-- #380 - rename SPARQLQueryDefinition.setOptimzeLevel to setOptimizeLevel
-- #392 - add DocumentWriteSet.addAs methods
-- #432 - a more portable variant to initialize (and teardown) a test server
-- #433 - moving JAXBContext initialization into a static, lazily initialized field
-- #434 - pass thru full response body when an error message doesn't conform to expected formats
-- #437 - fix support for Date range queries; upgrade to latest Jackson
-- #467 - call shutdown on ThreadSafeClientConnManager (the HTTP connection pool) to avoid any lingering connections in CLOSE_WAIT
-- #472 - remove unnecessary INFO logging from RuleDefinition
+- [#380](https://github.com/marklogic/java-client-api/issues/380) - rename SPARQLQueryDefinition.setOptimzeLevel to setOptimizeLevel
+- [#392](https://github.com/marklogic/java-client-api/issues/392) - add DocumentWriteSet.addAs methods
+- [#432](https://github.com/marklogic/java-client-api/issues/432) - a more portable variant to initialize (and teardown) a test server
+- [#433](https://github.com/marklogic/java-client-api/issues/433) - moving JAXBContext initialization into a static, lazily initialized field
+- [#434](https://github.com/marklogic/java-client-api/issues/434) - pass thru full response body when an error message doesn't conform to expected formats
+- [#437](https://github.com/marklogic/java-client-api/issues/437) - fix support for Date range queries; upgrade to latest Jackson
+- [#467](https://github.com/marklogic/java-client-api/issues/467) - call shutdown on ThreadSafeClientConnManager (the HTTP connection pool) to avoid any lingering connections in CLOSE_WAIT
+- [#472](https://github.com/marklogic/java-client-api/issues/472) - remove unnecessary INFO logging from RuleDefinition
 - expose PojoRepository.getId
 - full list [here](https://github.com/marklogic/java-client-api/compare/3.0.5...3.0.6)
 
 ### 3.0.5
 
 - some javadoc improvements and code/test cleanup
-- #176 - deprecate QueryOptionsHandle since it depends on QueryOptions which is already deprecated
+- [#176](https://github.com/marklogic/java-client-api/issues/176) - deprecate QueryOptionsHandle since it depends on QueryOptions which is already deprecated
 - #261, #266, #382, #388, and #390 - fix several errors when woodstox is used
-- #364 and #381 - respect all cookies (including load-balancer created cookies) when Transaction is used
+- [#364](https://github.com/marklogic/java-client-api/issues/364) and #381 - respect all cookies (including load-balancer created cookies) when Transaction is used
 - add method ServerTransform.addParameter
-- #378 - add DATE type support to RDFTypes
-- #396 - fix DocumentManager.write(DocumentWriteSet, ServerTransform, Transaction) to use ServerTransform
-- #395 - fix RuleManager.matchAs(content, ruleListHandle) which was throwing NPE
+- [#378](https://github.com/marklogic/java-client-api/issues/378) - add DATE type support to RDFTypes
+- [#396](https://github.com/marklogic/java-client-api/issues/396) - fix DocumentManager.write(DocumentWriteSet, ServerTransform, Transaction) to use ServerTransform
+- [#395](https://github.com/marklogic/java-client-api/issues/395) - fix RuleManager.matchAs(content, ruleListHandle) which was throwing NPE
 - full list [here](https://github.com/marklogic/java-client-api/compare/3.0.4...3.0.5)
 
 ### 3.0.4