Squashed 'core/' changes from 340e7ce..e7c41bb

e7c41bb Merge branch 'develop' of github.com:syncany/syncany into develop
3b3c3ce Add a few tests, update changelog
7908dc1 Flushing to prevent corruption
78c86c2 use of bitcoinj file
f072785 * remove trailing "/" from base58 alphabet (initially added beacause I thought I had to decrypt master/config ...... my mistake) * modify link regex to parse correctly syncany links
dbaf672 clean up
9b1153e found it
5c4bf2f problem with GenlinkCommandTest, sometimes failing, sometimes succeeding
19fc4ae Update CHANGELOG.md
9b75f3a Update CHANGELOG.md
320ca98 Fixing test: There are more folders due to transactions
8e63b54 Merge pull request #224 from syncany/feature/atomic-operations
20ab344 Making actionFileHandler tx-unaware
dbf4cfe test
8be7e8c Add flag for 'do not remove temp files, relates to #64'
51e9aa7 Move some comments
b79a96a Update changelog
d04f4b9 Merge branch 'develop' into feature/atomic-operations
236b5dc Delete multichunk from cache if decryption failed. Related to #59
569cccf Merge branch 'develop' into feature/atomic-operations
32cf5c0 Delete multichunk from cache if decryption failed. Related to #59
8bab6a8 Merge branch 'develop' into feature/atomic-operations
2d6cb9f Delete multichunk from cache if decryption failed. Related to #59
7404ca0 Merge branch 'develop' into feature/atomic-operations
daacbad Delete multichunk from cache if decryption failed. Related to #59
dd3f3ae First check for native Java, relates to #221 #222
8d90769 Hopefully fix #221
8782615 Try to fix issue #221
4cc5de2 Moving unreferenced deletions out of transactions and test for it
c3558ba Formatting, grouping, commenting
442a983 Cleaning unreferenced temporary files
da964b2 Split cleanTransactions in another function
35c7f0f Extracting cleanTransactions from TransferManager
eaccbe2 Moving temporary files to seperate directory
24b697b Reordering RemoteTransaction (no code changes, just ordering and grouping); moving Storage* to transfer package
006d98b Merge branch 'develop' into feature/atomic-operations
3ec7846 Testing list() and download()
ec4a077 Merge branch 'develop' of github.com:syncany/syncany into develop
b99ab47 Add new readme with screenshots of user guide and add a few authors
e1ff548 Second cleanup test
afbbbb9 First cleanup interrupted test
14182e5 Don't retry if a file does not exist
de573fd Updating TransferManager javadoc to reflect new situation
5a14f09 Bumping arch PKGBUILD
8f788db Updated changelog
7261b48 Re-merge develop
9bcb25a Fix 4_1 assumptions, and assumption issues in 4_3, relates to #64
2904e0f Merging develop into feature/atomic-operations
bff2e70 Moving dummy file download to TxAwareTM.
c53ec5b Attempting to make unreliable tests more consistent
b8ec626 Update CHANGELOG.md
de5a5b6 Write full daemon-example.xml instead of almost empty one
453feae Add man page / help text for 'sy daemon'
24d98a2 Fix force-stop issue on Linux and Mac(?)
7dcb3f8 Starting with extracting functionality to TransactionAwareTM
f521ce0 Fixing autoformat eclipse
aea7384 Deleting transaction file before final deletions
4f3984f Add log level to bash completion
d47e82d Further enhance the bash completion script
e50fbfd Merge branch 'develop' of github.com:syncany/syncany into develop
8fbdf5a Rewrite bash completion; fixes #209
71d27aa Merge pull request #218 from vwiencek/quick-fix
77715dc missing break
bf907af Merge branch 'develop' of https://github.com/syncany/syncany into develop
02ee5b0 Update CHANGELOG.md
5194879 Merge branch 'develop' into feature/initautoadd
ddba59a Merge branch 'feature/scripts' into develop
08569c5 Quick fix to include sy.bat; relates to #210
2ed8b49 Commenting
4adb609 * move .bat to .skel.bat * embedde daemon script into main script with goto/labels
9851464 Merge develop
1f92cf6 Automatically add folder to daemon config in sy init/connect
f5aa457 correct call to daemon_get_pid
a215491 Minor things
9cee132 Update CHANGELOG.md
2f176e0 Prettify combined Linux script
18f9f14 Merge branch 'develop' into HEAD
36cdd81 remove circular reference
8d5dc84 Fixes basic daemon test, closes #185
e6cc901 sy script now includes daemon handling
bc9c641 Do not automatically att ~/Syncany to daemon.xml; create daemon-example.xml instead; relates to #210
f80342e merge daemon in lib
b39c48d sy and syd merged
f027082 Remove wrong comment
e704f4c Added test for TX that fails twice; test fails; refactoring
e5d293b Adding comment
08a7de1 Add test for atomic transactions; works as expected (more tests required though); relates to #64
1d88c08 Renaming, beginning unit test preparation
db4984e Merged develop
83dfe00 Update readme
a0a1c3f Merge branch 'develop' of github.com:syncany/syncany into develop
9ecd4cc Update README.md
b65b741 Update README.md
fb597e5 Smaller readme with images
8229b36 Smaller readme with images
97ec8d8 Smaller readme with images
54a9cac Smaller readme with images
c5c6b13 Smaller readme with images
f45c2b3 Bump version
656d530 small correction
362f1eb remove function keyword
e52e3bb remove darwin detection
042785d add generic get_realpath function
c1750f6 detect osx
e115634 script working with OS X
42b92c5 revert
e8caf24 update script to work with osx
7d93830 Merge branch 'develop' of https://github.com/syncany/syncany into develop
da6e4f5 Update README.md
6ff3f28 Bump version in readme
ae1b08d Merge branch 'release/0.1.9-alpha'
4b2cc32 Userguide to changelog
c241f5e Update README.md
5a9cce6 Update README.md
3adaf2c Merge branch 'develop' of https://github.com/syncany/syncany into develop
39ba4cd Move syncany-assets to https://github.com/syncany/syncany-assets
67df3d7 Move syncany-assets to https://github.com/syncany/syncany-assets
d642689 Add new diagrams for documentation
6ab48f9 Merge branch 'develop' of https://github.com/syncany/syncany into develop
af27968 Uncomment cleanup in tests
965cd65 Merge develop
6a22c95 Add no-CLI-while-syncing tests
8b6b6e5 Fix bash completion generation on Travi
832191d Fix? the usual suspects by increasing the sleep times a bit
5d8430c You won't believe how I fixed this bug.
296264d Livin' on the edge.
d10e872 Wrong Arrays class
52101f7 Checksum checking when assembling files
6b2d13a Unused code in test
7f8d39d Rolling back local database if cleanup fails (fixes test)
ac91278 Added a test; should this fail?
ad1ac2f Encrypting transaction files and adding config to transfermanager
e43a078 Merge branch 'feature/atomic-operations' of github.com:syncany/syncany into feature/atomic-operations
919da59 Fix switch/case fallthrough in CLI output2
7dc47f2 Fixing cleanupTransactions to undo deletes
9b1a26f Add specification for TM.download()
6530e07 Making plugins almost entirely tx-agnostic
30a9d48 Commenting and removing legacy code
a68b4e6 Formatting
d5f5c71 Merge develop; TX.add -> TX.upload
102b093 Merge branch 'feature/atomic-operations' of https://github.com/syncany/syncany into feature/atomic-operations
f21cf91 Fixing tests after rename
3a9581c Refactoring createRemoteFile; getting rid of warnings
081298e formatting adjustments
d655c7c Formatting stuff
90e8bde Using name patterns to dynamically create remotefiles
c05c081 Update CHANGELOG.md
89076f0 Fixes issue #200
f48f947 Quick fix for issue #200
8d28191 Merging develop into feature/atomic-operations
23b0d14 Merge branch 'develop' into feature/atomic-operations
3a01307 Merge pull request #202 from syncany/bugfix/cleanup-time
c401715 Making cleanup time hold for entire operation
bc769fa Make bash completion awesome.
bb53537 Merge again?\!
b9996c9 Merged develop into atomic operations; issue with Reflections
fa10785 Two unit tests were failing. You won't believe how I fixed it!
a74bdc7 Changelog update
e79981b Implement bash completion; relates to #201
181036d Add help text 'sy ls' to overview
81a4ce5 Add help text 'sy ls' to overview
8964344 Merge pull request #196 from syncany/feature/daemonauth
3ed505a Merge commit 'b9a500c23d23632d040ce5d62b716049dd882c25' into feature/atomic-operations
b9a500c Fixing move used in deletion to not fail if original did not exist
c168fd3 Add comments for #184 #196
a12bca3 Remove '*' logic from CLI HTTPS client; Add AllowAllHostnamesVerifier(); only connect to localhost; relates to #196 #184
7e7fd38 Unignoring deletes in transaction
42f32c5 Transactionifying the transaction cleanup
aab1d9a Removing empty lines
7d4f8fc Reproduces issue #200
97b6b54 Merge branch 'develop' into feature/daemonauth
5ce98fe Small fixes with regards to cleaning
c85ae4b Enabling atomic cleanup
aa856b4 Patching tests
46a2a68 Refactoring and enabling cleanup
206698a Refactoring TransactionTO for better generalization
1a30096 Going wild with new lines
15b1e9f Add bind addr/port to daemon config; implement auto certificate regeneration on CN change; relates to #184 #196
f796f9a Deleting duplicate files, fixing test and restoring some infrastructure
de47aa8 Merging develop into feature/atomic-operations
4388a1b Atomicity Up, initial attempt
7bdba7f Merge branch 'develop' into feature/daemonauth
1de7d10 Re-adding move methods to TM's
3f52e32 Merge branch 'develop' into feature/atomic-operations
c452952 Merge pull request #198 from syncany/bugfix/cleanup-when
a410b98 Small fixes on tests et al.
b4b1a46 Updating Cleanup usage with new options
e0bda79 New cleanup options tests
a4eadaf Merge branch 'develop' into feature/daemonauth
f698d3d Remove unused code
1da0e71 Alter reflections comment
0a10f85 Remove Reflections library in favor of Guava
ff5d798 Various style/small fixes
07a2eef Philipp dormiens nunquam titillandus. (newlines)
9183604 Enabling options in CLI
badb05d Adding time and number of db-file options to CleanupOptions
a740db9 Moving Port file and creating Cleanup file in state directory
1fb392f Update changelog
7d47d0c Remove BC 'ext' JAR (saves 2.9MB)
807adf4 Merge branch 'develop' into feature/daemonauth
607fc18 Merge branch 'develop' of github.com:syncany/syncany into develop
4845f69 Fixes wildcard-CN issue with CLI-to-API communication; daemonauth is now ready for merge; relates to #184
8b1834a Add self-signed ceritificate generation for keystore, add HTTPS only for API + web interface, almost have CLI-to-API working (HTTPS trust issue)
a47fc1d Move keystore to UserConfig
81bb916 Implement cache size parameter configurability
8275757 Revert "Use non-zero exit code on error"
2abf2fa Use non-zero exit code on error
0657939 Merge pull request #194 from syncany/bugfix/daemon-test
65f1deb Fixes LRU cache, fixes #169
e66bc4a Fix first of two tests dependant on number of database versions
f1c2388 Increasing time to allow settling and small altering cleanup
f980458 Bump PKGBUILD version
0ba5dac Bump version again; merge full cleanup, adjust changelog
a48d438 Merge branch 'develop' into bugfix/full-cleanup
d282c4f Merge branch 'release/0.1.8-alpha' into develop
2978c28 Fix command line test and CLI cleanup output to reflect new cleanup
edf841d Cleanup all databases to remove dirty references
2456885 Adjusting tests for full cleanup (all databaseversions are removed)
121fa8b disable filterFileVersion
abd4f4a Sorting list and fixing test
93f5b91 Removing MIN_KEEP_DATABASE_VERSIONS
4680449 Switch cleanup operation to full
0a5141e Merge branch 'feature/daemonauth' of github.com:syncany/syncany into feature/daemonauth
2fafb1f Merge develop into auth branch
e163386 Merge branch 'feature/daemonauth' of github.com:syncany/syncany into feature/daemonauth
7586cdd Merge branch 'feature/daemon' into feature/daemonauth
4165ecf Merge branch 'feature/daemon' into feature/daemonauth
ed6b1ee Merge branch 'develop' into feature/daemonauth
ffa3f66 Merge branch 'feature/daemonauth' of github.com:syncany/syncany into feature/daemonauth
f2b63fe Formatting
c370fac Merge branch 'feature/daemon' into feature/daemonauth
a87ec4a Merge branch 'develop' into feature/daemonauth
9bb3705 Merge branch 'develop' into feature/daemonauth
7449f4f HTTPS-only for web interface and API
3e128e0 Naming, rest of review, NICE WORK
699ca5b Merge branch 'develop' into feature/atomic-operations
1921a38 Tiny alterations on the atomic operations; untested
dfcc4f8 Merge branch 'feature/atomic-operations' of github.com:pimotte/syncany into feature/atomic-operations
c837613 Transaction test
7d04455 Ensuring files are listed after cleaning up the repo
fc48e15 Merge remote-tracking branch 'upstream/develop' into feature/atomic-operations
d269651 Revert "Enabling atomic deletes" and the two following commits that enabled atomic cleanup.
b498065 Fixing nullpointers and such
5115152 Atomic cleanup
9a20c17 Enabling atomic deletes
8f57cdd Fixing tests for presence of temp directory
16ce66a Merge remote-tracking branch 'upstream/develop' into feature/atomic-operations
01a2e02 Fix NullPointerException with config
79a2481 Adding config to connection
3cc4797 Remote file creation and unreliable-plugin move implementation
4b49587 Using cache for transaction files
5c3a477 Each machine cleans up their own mess
047be4c Don't ignore transaction files to prevent stackoverflow
b58893c Ignore files in list if they are in transaction
b909598 Merge remote-tracking branch 'upstream/develop' into feature/atomic-operations
97af2d3 Writing the transaction to a file
516684b Merge remote-tracking branch 'upstream/develop' into feature/atomic-operations
1d18160 Switching UpOperation to atomic transfer
d912092 Creating a transaction file in the remote repo
15f437c Adding move to interface
c9a5c8d First version TempRemoteFile
63d1d6c First draft RemoteTransaction

git-subtree-dir: core
git-subtree-split: e7c41bbedcba2659ec4629347a4b2dd606ad0de6
Merge commit '4f3067892440cc965374725a191634aab229e2a7' into develop
Bump version, adjustments for atomic ops