ErrorProne: Enable and fix UnusedException check

Enable UnusedException at ERROR level which causes the build to fail
in many places with:

  [UnusedException] This catch block catches an symbol and re-throws
  another, but swallows the caught symbol rather than setting it as a
  cause. This can make debugging harder.

Fix it by setting the caught exception as cause on the subsequently
thrown exception.

Note: The grammatically incorrect error message is copy-pasted as-is
from the version of ErrorProne currently used in Bazel; it has been
fixed by [1] in the latest version.

[1] https://github.com/google/error-prone/commit/d57a39c

Change-Id: I11ed38243091fc12f64f1b2db404ba3f1d2e98b5
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

34 files changed, 141 insertions, 69 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index 5232223c4c..eef7940012 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -160,7 +160,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 			verifyDirectories(u);
 		} catch (URISyntaxException e) {
 			throw new InvalidRemoteException(
-					MessageFormat.format(JGitText.get().invalidURL, uri));
+					MessageFormat.format(JGitText.get().invalidURL, uri), e);
 		}
 		@SuppressWarnings("resource") // Closed by caller
 		Repository repository = init();
@@ -180,8 +180,9 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 				repository.close();
 			}
 			cleanup();
-			throw new InvalidRemoteException(MessageFormat.format(
-					JGitText.get().invalidRemote, remote));
+			throw new InvalidRemoteException(
+					MessageFormat.format(JGitText.get().invalidRemote, remote),
+					e);
 		} catch (GitAPIException | RuntimeException e) {
 			if (repository != null) {
 				repository.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
index a4b9bcf00e..033dd60c3b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
@@ -223,7 +223,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 					e.getMessage(), e);
 		} catch (URISyntaxException e) {
 			throw new InvalidRemoteException(MessageFormat.format(
-					JGitText.get().invalidRemote, remote));
+					JGitText.get().invalidRemote, remote), e);
 		} catch (NotSupportedException e) {
 			throw new JGitInternalException(
 					JGitText.get().exceptionCaughtDuringExecutionOfFetchCommand,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
index 12517df516..a4ca309095 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
@@ -180,7 +180,7 @@ public class LsRemoteCommand extends
 			}
 		} catch (URISyntaxException e) {
 			throw new InvalidRemoteException(MessageFormat.format(
-					JGitText.get().invalidRemote, remote));
+					JGitText.get().invalidRemote, remote), e);
 		} catch (NotSupportedException e) {
 			throw new JGitInternalException(
 					JGitText.get().exceptionCaughtDuringExecutionOfLsRemoteCommand,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
index b9b15ebdc6..aa5a63499c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
@@ -152,8 +152,9 @@ public class PushCommand extends
 			}
 
 		} catch (URISyntaxException e) {
-			throw new InvalidRemoteException(MessageFormat.format(
-					JGitText.get().invalidRemote, remote));
+			throw new InvalidRemoteException(
+					MessageFormat.format(JGitText.get().invalidRemote, remote),
+					e);
 		} catch (TransportException e) {
 			throw new org.eclipse.jgit.api.errors.TransportException(
 					e.getMessage(), e);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
index fcfae65bc6..fb6e5df589 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
@@ -350,6 +350,7 @@ public class SimilarityIndex {
 		return (1 << idHashBits) * (idHashBits - 3) / idHashBits;
 	}
 
+	@SuppressWarnings("UnusedException")
 	private void grow() throws TableFullException {
 		if (idHashBits == 30)
 			throw new TableFullException();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
index 023efd8e17..6a2c3898a6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
@@ -139,7 +139,7 @@ public class ManifestParser extends DefaultHandler {
 		try {
 			xr = XMLReaderFactory.createXMLReader();
 		} catch (SAXException e) {
-			throw new IOException(JGitText.get().noXMLParserAvailable);
+			throw new IOException(JGitText.get().noXMLParserAvailable, e);
 		}
 		xr.setContentHandler(this);
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
index 98f61d1597..c039aaffa9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
@@ -541,7 +541,7 @@ public class RepoCommand extends GitCommand<RevCommit> {
 				inputStream = new FileInputStream(manifestPath);
 			} catch (IOException e) {
 				throw new IllegalArgumentException(
-						JGitText.get().pathNotConfigured);
+						JGitText.get().pathNotConfigured, e);
 			}
 		}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
index ad7aebc27f..3b94984561 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
@@ -290,9 +290,12 @@ public class FsckPackParser extends PackParser {
 							ErrorType.MISMATCH_CRC);
 				}
 			} catch (MissingObjectException e) {
-				throw new CorruptPackIndexException(MessageFormat
-						.format(JGitText.get().missingCRC, entry.getName()),
+				CorruptPackIndexException cpe = new CorruptPackIndexException(
+						MessageFormat.format(JGitText.get().missingCRC,
+								entry.getName()),
 						ErrorType.MISSING_CRC);
+				cpe.initCause(e);
+				throw cpe;
 			}
 		}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
index bee2e01a83..6e7ad3e613 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
@@ -236,7 +236,7 @@ public class DfsBlockCacheConfig {
 						JGitText.get().enumValueNotSupported3,
 						CONFIG_CORE_SECTION,
 						CONFIG_DFS_SECTION,
-						CONFIG_KEY_STREAM_RATIO, v));
+						CONFIG_KEY_STREAM_RATIO, v), e);
 			}
 		}
 		return this;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
index 857c1730f4..169587081c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
@@ -769,7 +769,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 						shallowCommitsIds.add(ObjectId.fromString(line));
 					} catch (IllegalArgumentException ex) {
 						throw new IOException(MessageFormat
-								.format(JGitText.get().badShallowLine, line));
+								.format(JGitText.get().badShallowLine, line),
+								ex);
 					}
 				}
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
index 0de818a1db..984c163664 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
@@ -1071,7 +1071,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 		} catch (DataFormatException e) {
 			throw new CorruptObjectException(MessageFormat.format(
 					JGitText.get().objectAtHasBadZlibStream, Long.valueOf(pos),
-					getPackFile()));
+					getPackFile()), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index b636db6f2a..fddd430bf1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -1035,7 +1035,10 @@ public class RefDirectory extends RefDatabase {
 					lck.waitForStatChange();
 				} catch (InterruptedException e) {
 					lck.unlock();
-					throw new ObjectWritingException(MessageFormat.format(JGitText.get().interruptedWriting, name));
+					throw new ObjectWritingException(
+							MessageFormat.format(
+									JGitText.get().interruptedWriting, name),
+							e);
 				}
 				if (!lck.commit())
 					throw new ObjectWritingException(MessageFormat.format(JGitText.get().unableToWrite, name));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
index 743badbccb..bf47d2c3cd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
@@ -149,8 +149,10 @@ public class UnpackedObject {
 			}
 			return new LargeObject(type, size, path, id, wc.db);
 		} catch (ZipException badStream) {
-			throw new CorruptObjectException(id,
+			CorruptObjectException coe = new CorruptObjectException(id,
 					JGitText.get().corruptObjectBadStream);
+			coe.initCause(badStream);
+			throw coe;
 		}
 	}
 
@@ -192,8 +194,10 @@ public class UnpackedObject {
 			}
 			return size;
 		} catch (ZipException badStream) {
-			throw new CorruptObjectException(id,
+			CorruptObjectException coe = new CorruptObjectException(id,
 					JGitText.get().corruptObjectBadStream);
+			coe.initCause(badStream);
+			throw coe;
 		}
 	}
 
@@ -205,8 +209,10 @@ public class UnpackedObject {
 			try {
 				r = inf.inflate(buf);
 			} catch (DataFormatException e) {
-				throw new CorruptObjectException(id,
+				CorruptObjectException coe = new CorruptObjectException(id,
 						JGitText.get().corruptObjectBadStream);
+				coe.initCause(e);
+				throw coe;
 			}
 			if (r != 0)
 				throw new CorruptObjectException(id,
@@ -277,8 +283,10 @@ public class UnpackedObject {
 						remaining -= r;
 					return r;
 				} catch (ZipException badStream) {
-					throw new CorruptObjectException(id,
+					CorruptObjectException coe = new CorruptObjectException(id,
 							JGitText.get().corruptObjectBadStream);
+					coe.initCause(badStream);
+					throw coe;
 				}
 			}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
index 33ffe07176..9a6ec760b6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
@@ -1579,8 +1579,8 @@ public class PackWriter implements AutoCloseable {
 						if (pool.awaitTermination(60, TimeUnit.SECONDS))
 							break;
 					} catch (InterruptedException e) {
-						throw new IOException(
-								JGitText.get().packingCancelledDuringObjectsWriting);
+						throw new IOException(JGitText
+								.get().packingCancelledDuringObjectsWriting, e);
 					}
 				}
 			}
@@ -1604,7 +1604,8 @@ public class PackWriter implements AutoCloseable {
 				// Cross our fingers and just break out anyway.
 				//
 				throw new IOException(
-						JGitText.get().packingCancelledDuringObjectsWriting);
+						JGitText.get().packingCancelledDuringObjectsWriting,
+						ie);
 			}
 		}
 
@@ -1645,7 +1646,7 @@ public class PackWriter implements AutoCloseable {
 			for (Future<?> f : futures)
 				f.cancel(true);
 			throw new IOException(
-					JGitText.get().packingCancelledDuringObjectsWriting);
+					JGitText.get().packingCancelledDuringObjectsWriting, ie);
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
index 20066bec78..d0e24413bb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
@@ -165,9 +165,10 @@ public class SubmoduleValidator {
 				}
 			}
 		} catch (ConfigInvalidException e) {
-			throw new SubmoduleValidationException(
-					JGitText.get().invalidGitModules,
-					GITMODULES_PARSE);
+			SubmoduleValidationException sve = new SubmoduleValidationException(
+					JGitText.get().invalidGitModules, GITMODULES_PARSE);
+			sve.initCause(e);
+			throw sve;
 		}
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
index a5e4d787f4..dc5e5cc20f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
@@ -114,8 +114,11 @@ public final class AbbreviatedObjectId implements Serializable {
 			final int d = hexUInt32(bs, ptr + 24, end);
 			final int e = hexUInt32(bs, ptr + 32, end);
 			return new AbbreviatedObjectId(end - ptr, a, b, c, d, e);
-		} catch (ArrayIndexOutOfBoundsException e1) {
-			throw new InvalidObjectIdException(bs, ptr, end - ptr);
+		} catch (ArrayIndexOutOfBoundsException e) {
+			InvalidObjectIdException e1 = new InvalidObjectIdException(bs, ptr,
+					end - ptr);
+			e1.initCause(e);
+			throw e1;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
index d502274c43..ffc742d473 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
@@ -601,7 +601,10 @@ public final class Constants {
 				throw new CorruptObjectException(id, JGitText.get().corruptObjectInvalidType);
 			}
 		} catch (ArrayIndexOutOfBoundsException bad) {
-			throw new CorruptObjectException(id, JGitText.get().corruptObjectInvalidType);
+			CorruptObjectException coe = new CorruptObjectException(id,
+					JGitText.get().corruptObjectInvalidType);
+			coe.initCause(bad);
+			throw coe;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
index abc9b21196..cc0b995f10 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
@@ -46,7 +46,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 			return StringUtils.toBoolean(n);
 		} catch (IllegalArgumentException err) {
 			throw new IllegalArgumentException(MessageFormat.format(
-					JGitText.get().invalidBooleanValue, section, name, n));
+					JGitText.get().invalidBooleanValue, section, name, n), err);
 		}
 	}
 
@@ -152,7 +152,8 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 			return mul * Long.parseLong(n);
 		} catch (NumberFormatException nfe) {
 			throw new IllegalArgumentException(MessageFormat.format(
-					JGitText.get().invalidIntegerValue, section, name, str));
+					JGitText.get().invalidIntegerValue, section, name, str),
+					nfe);
 		}
 	}
 
@@ -239,7 +240,10 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 			return wantUnit.convert(Long.parseLong(digits) * inputMul,
 					inputUnit);
 		} catch (NumberFormatException nfe) {
-			throw notTimeUnit(section, subsection, unitName, valueString);
+			IllegalArgumentException iae = notTimeUnit(section, subsection,
+					unitName, valueString);
+			iae.initCause(nfe);
+			throw iae;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/MutableObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/MutableObjectId.java
index 86b306d5b5..4a712ba360 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/MutableObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/MutableObjectId.java
@@ -234,9 +234,11 @@ public class MutableObjectId extends AnyObjectId {
 			w3 = RawParseUtils.parseHexInt32(bs, p + 16);
 			w4 = RawParseUtils.parseHexInt32(bs, p + 24);
 			w5 = RawParseUtils.parseHexInt32(bs, p + 32);
-		} catch (ArrayIndexOutOfBoundsException e1) {
-			throw new InvalidObjectIdException(bs, p,
+		} catch (ArrayIndexOutOfBoundsException e) {
+			InvalidObjectIdException e1 = new InvalidObjectIdException(bs, p,
 					Constants.OBJECT_ID_STRING_LENGTH);
+			e1.initCause(e);
+			throw e1;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
index 11c0aefe39..269049f4a2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
@@ -213,9 +213,11 @@ public class ObjectId extends AnyObjectId implements Serializable {
 			final int d = RawParseUtils.parseHexInt32(bs, p + 24);
 			final int e = RawParseUtils.parseHexInt32(bs, p + 32);
 			return new ObjectId(a, b, c, d, e);
-		} catch (ArrayIndexOutOfBoundsException e1) {
-			throw new InvalidObjectIdException(bs, p,
+		} catch (ArrayIndexOutOfBoundsException e) {
+			InvalidObjectIdException e1 = new InvalidObjectIdException(bs, p,
 					Constants.OBJECT_ID_STRING_LENGTH);
+			e1.initCause(e);
+			throw e1;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index 503e218b5a..a7a832c1aa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -550,9 +550,11 @@ public abstract class Repository implements AutoCloseable {
 						try {
 							pnum = Integer.parseInt(parentnum);
 						} catch (NumberFormatException e) {
-							throw new RevisionSyntaxException(
+							RevisionSyntaxException rse = new RevisionSyntaxException(
 									JGitText.get().invalidCommitParentNumber,
 									revstr);
+							rse.initCause(e);
+							throw rse;
 						}
 						if (pnum != 0) {
 							RevCommit commit = (RevCommit) rev;
@@ -647,8 +649,10 @@ public abstract class Repository implements AutoCloseable {
 					try {
 						dist = Integer.parseInt(distnum);
 					} catch (NumberFormatException e) {
-						throw new RevisionSyntaxException(
+						RevisionSyntaxException rse = new RevisionSyntaxException(
 								JGitText.get().invalidAncestryLength, revstr);
+						rse.initCause(e);
+						throw rse;
 					}
 				} else
 					dist = 1;
@@ -707,7 +711,10 @@ public abstract class Repository implements AutoCloseable {
 							remoteConfig = new RemoteConfig(getConfig(),
 									"origin"); //$NON-NLS-1$
 						} catch (URISyntaxException e) {
-							throw new RevisionSyntaxException(revstr);
+							RevisionSyntaxException rse = new RevisionSyntaxException(
+									revstr);
+							rse.initCause(e);
+							throw rse;
 						}
 						String remoteBranchName = getConfig()
 								.getString(
@@ -874,8 +881,11 @@ public abstract class Repository implements AutoCloseable {
 		try {
 			number = Integer.parseInt(time);
 		} catch (NumberFormatException nfe) {
-			throw new RevisionSyntaxException(MessageFormat.format(
-					JGitText.get().invalidReflogRevision, time));
+			RevisionSyntaxException rse = new RevisionSyntaxException(
+					MessageFormat.format(JGitText.get().invalidReflogRevision,
+							time));
+			rse.initCause(nfe);
+			throw rse;
 		}
 		assert number >= 0;
 		ReflogReader reader = getReflogReader(ref.getName());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
index a177c290ee..1e7f3b1f00 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
@@ -655,7 +655,8 @@ public class AmazonS3 {
 					try {
 						xr = XMLReaderFactory.createXMLReader();
 					} catch (SAXException e) {
-						throw new IOException(JGitText.get().noXMLParserAvailable);
+						throw new IOException(
+								JGitText.get().noXMLParserAvailable, e);
 					}
 					xr.setContentHandler(this);
 					try (InputStream in = c.getInputStream()) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
index 8604244db4..1417faee80 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
@@ -203,7 +203,9 @@ abstract class BasePackConnection extends BaseConnection {
 			try {
 				id  = ObjectId.fromString(line.substring(0, 40));
 			} catch (InvalidObjectIdException e) {
-				throw invalidRefAdvertisementLine(line);
+				PackProtocolException ppe = invalidRefAdvertisementLine(line);
+				ppe.initCause(e);
+				throw ppe;
 			}
 			if (name.equals(".have")) { //$NON-NLS-1$
 				additionalHaves.add(id);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
index 93800d5009..c992bb1cb5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
@@ -286,7 +286,7 @@ public class PacketLineIn {
 		try {
 			len = RawParseUtils.parseHexInt16(lineBuffer, 0);
 		} catch (ArrayIndexOutOfBoundsException err) {
-			throw invalidHeader();
+			throw invalidHeader(err);
 		}
 
 		if (len == 0) {
@@ -320,6 +320,12 @@ public class PacketLineIn {
 				+ (char) lineBuffer[2] + (char) lineBuffer[3]));
 	}
 
+	private IOException invalidHeader(Throwable cause) {
+		IOException ioe = invalidHeader();
+		ioe.initCause(cause);
+		return ioe;
+	}
+
 	/**
 	 * IOException thrown by read when the configured input limit is exceeded.
 	 *
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
index 24cd8f3df1..e505e1706f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
@@ -2110,7 +2110,7 @@ public class ReceivePack {
 		} catch (InputOverLimitIOException e) {
 			String msg = JGitText.get().tooManyCommands;
 			fatalError(msg);
-			throw new PackProtocolException(msg);
+			throw new PackProtocolException(msg, e);
 		} finally {
 			try {
 				close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
index 13b891fcfc..c6ecb3a79f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
@@ -140,7 +140,7 @@ public class TestProtocol<C> extends TransportProtocol {
 			int n = handles.size();
 			uri = new URIish(SCHEME + "://test/conn" + n); //$NON-NLS-1$
 		} catch (URISyntaxException e) {
-			throw new IllegalStateException();
+			throw new IllegalStateException(e);
 		}
 		handles.put(uri, new Handle(req, remote));
 		return uri;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
index 155c115f82..04ebddb107 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
@@ -113,7 +113,10 @@ class TransportBundleFile extends Transport implements TransportBundle {
 		try {
 			src = new FileInputStream(bundle);
 		} catch (FileNotFoundException err) {
-			throw new TransportException(uri, JGitText.get().notFound);
+			TransportException te = new TransportException(uri,
+					JGitText.get().notFound);
+			te.initCause(err);
+			throw te;
 		}
 		return new BundleFetchConnection(this, src);
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
index be17b44d79..403f98d869 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
@@ -143,7 +143,10 @@ class TransportLocal extends Transport implements PackTransport {
 					.setFS(local != null ? local.getFS() : FS.DETECTED)
 					.setGitDir(remoteGitDir).build();
 		} catch (IOException err) {
-			throw new TransportException(uri, JGitText.get().notAGitDirectory);
+			TransportException te = new TransportException(uri,
+					JGitText.get().notAGitDirectory);
+			te.initCause(err);
+			throw te;
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
index 6ebb668c7a..858d1f7b6a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
@@ -266,7 +266,10 @@ public class URIish implements Serializable {
 				try {
 					val = parseHexByte(c1, c2);
 				} catch (ArrayIndexOutOfBoundsException e) {
-					throw new URISyntaxException(s, JGitText.get().cannotParseGitURIish);
+					URISyntaxException use = new URISyntaxException(s,
+							JGitText.get().cannotParseGitURIish);
+					use.initCause(e);
+					throw use;
 				}
 				os[j++] = (byte) val;
 				i += 2;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
index 1880c8b733..df9f11ecf8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
@@ -282,9 +282,12 @@ abstract class WalkEncryption {
 		String REGEX_TRANS = "(.+)/(.+)/(.+)"; //$NON-NLS-1$
 	}
 
-	static GeneralSecurityException securityError(String message) {
-		return new GeneralSecurityException(
+	static GeneralSecurityException securityError(String message,
+			Throwable cause) {
+		GeneralSecurityException e = new GeneralSecurityException(
 				MessageFormat.format(JGitText.get().encryptionError, message));
+		e.initCause(cause);
+		return e;
 	}
 
 	/**
@@ -332,21 +335,21 @@ abstract class WalkEncryption {
 			try {
 				size = Integer.parseInt(keySize);
 			} catch (Exception e) {
-				throw securityError(X_KEY_SIZE + EMPTY + keySize);
+				throw securityError(X_KEY_SIZE + EMPTY + keySize, e);
 			}
 
 			final int iter;
 			try {
 				iter = Integer.parseInt(keyIter);
 			} catch (Exception e) {
-				throw securityError(X_KEY_ITER + EMPTY + keyIter);
+				throw securityError(X_KEY_ITER + EMPTY + keyIter, e);
 			}
 
 			final byte[] salt;
 			try {
 				salt = Hex.decode(keySalt.replaceAll(REGEX_WS, EMPTY));
 			} catch (Exception e) {
-				throw securityError(X_KEY_SALT + EMPTY + keySalt);
+				throw securityError(X_KEY_SALT + EMPTY + keySalt, e);
 			}
 
 			KeySpec keySpec = new PBEKeySpec(pass.toCharArray(), salt, iter, size);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index 02ca86b954..2c3f3e2542 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -1159,7 +1159,7 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 			} catch (CharacterCodingException e) {
 				// This should so never happen.
 				throw new RuntimeException(MessageFormat.format(
-						JGitText.get().unencodeableFile, getName()));
+						JGitText.get().unencodeableFile, getName()), e);
 			}
 
 			encodedNameLen = b.limit();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
index fa99087fe4..4831fbb64e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
@@ -300,7 +300,8 @@ public class FileUtils {
 			} catch (InterruptedException e) {
 				throw new IOException(
 						MessageFormat.format(JGitText.get().renameFileFailed,
-								src.getAbsolutePath(), dst.getAbsolutePath()));
+								src.getAbsolutePath(), dst.getAbsolutePath()),
+						e);
 			}
 		}
 		throw new IOException(
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutInputStream.java
index 1356136000..1947b3bf04 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutInputStream.java
@@ -70,7 +70,7 @@ public class TimeoutInputStream extends FilterInputStream {
 			beginRead();
 			return super.read();
 		} catch (InterruptedIOException e) {
-			throw readTimedOut();
+			throw readTimedOut(e);
 		} finally {
 			endRead();
 		}
@@ -89,7 +89,7 @@ public class TimeoutInputStream extends FilterInputStream {
 			beginRead();
 			return super.read(buf, off, cnt);
 		} catch (InterruptedIOException e) {
-			throw readTimedOut();
+			throw readTimedOut(e);
 		} finally {
 			endRead();
 		}
@@ -102,7 +102,7 @@ public class TimeoutInputStream extends FilterInputStream {
 			beginRead();
 			return super.skip(cnt);
 		} catch (InterruptedIOException e) {
-			throw readTimedOut();
+			throw readTimedOut(e);
 		} finally {
 			endRead();
 		}
@@ -116,8 +116,11 @@ public class TimeoutInputStream extends FilterInputStream {
 		myTimer.end();
 	}
 
-	private InterruptedIOException readTimedOut() {
-		return new InterruptedIOException(MessageFormat.format(
-				JGitText.get().readTimedOut, Integer.valueOf(timeout)));
+	private InterruptedIOException readTimedOut(InterruptedIOException e) {
+		InterruptedIOException interrupted = new InterruptedIOException(
+				MessageFormat.format(JGitText.get().readTimedOut,
+						Integer.valueOf(timeout)));
+		interrupted.initCause(e);
+		return interrupted;
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutOutputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutOutputStream.java
index 7532c42b97..3fbf6ffdcb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutOutputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutOutputStream.java
@@ -72,7 +72,7 @@ public class TimeoutOutputStream extends OutputStream {
 			beginWrite();
 			dst.write(b);
 		} catch (InterruptedIOException e) {
-			throw writeTimedOut();
+			throw writeTimedOut(e);
 		} finally {
 			endWrite();
 		}
@@ -91,7 +91,7 @@ public class TimeoutOutputStream extends OutputStream {
 			beginWrite();
 			dst.write(buf, off, len);
 		} catch (InterruptedIOException e) {
-			throw writeTimedOut();
+			throw writeTimedOut(e);
 		} finally {
 			endWrite();
 		}
@@ -104,7 +104,7 @@ public class TimeoutOutputStream extends OutputStream {
 			beginWrite();
 			dst.flush();
 		} catch (InterruptedIOException e) {
-			throw writeTimedOut();
+			throw writeTimedOut(e);
 		} finally {
 			endWrite();
 		}
@@ -117,7 +117,7 @@ public class TimeoutOutputStream extends OutputStream {
 			beginWrite();
 			dst.close();
 		} catch (InterruptedIOException e) {
-			throw writeTimedOut();
+			throw writeTimedOut(e);
 		} finally {
 			endWrite();
 		}
@@ -131,8 +131,11 @@ public class TimeoutOutputStream extends OutputStream {
 		myTimer.end();
 	}
 
-	private InterruptedIOException writeTimedOut() {
-		return new InterruptedIOException(MessageFormat.format(
-				JGitText.get().writeTimedOut, Integer.valueOf(timeout)));
+	private InterruptedIOException writeTimedOut(InterruptedIOException cause) {
+		InterruptedIOException e = new InterruptedIOException(
+				MessageFormat.format(JGitText.get().writeTimedOut,
+						Integer.valueOf(timeout)));
+		e.initCause(cause);
+		return e;
 	}
 }