Use committer date instead of author date for Git epoch

Summary:
This is somewhat controversial but push date is usually more useful than commit date (which can be for example a month before other people can see the commit).
We can also store both dates.

Test Plan:
  git log --pretty="%ct %at"

Reviewers: epriestley

Reviewed By: epriestley

CC: nh, aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2319
Handle symbolic commit names better in Diffusion

Summary: We now allow symbolic commits, so let them through the pipeline.

Test Plan: {F10571}

Reviewers: davidreuss, btrahan, vrana

Reviewed By: davidreuss

CC: aran

Maniphest Tasks: T1130

Differential Revision: https://secure.phabricator.com/D2315
Fix DiffusionGitBrowseQuery to parse with "git config -l -f" instead of PHP ini parser

Summary: See discussion on rPc0aac8267dda74664acac5c93d9aeb5a0f9c4564.

Test Plan: Looked at externals/, got a correctly-behaving link.

Reviewers: vrana, davidreuss, btrahan

Reviewed By: vrana

CC: aran

Differential Revision: https://secure.phabricator.com/D2317
Fix paging for 'before ID' queries

Test Plan: https://secure.phabricator.com/paste/filter/all/?before=157 - 158 is missing.

Reviewers: epriestley

Reviewed By: epriestley

CC: aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2330
Create overview of Conduit methods

Summary:
Also couple of small changes:

- Add method name to title.
- 404 for /conduit/method/x/.
- Remove utilities from side panel.
- Remove side panel from log.

Test Plan:
/conduit/
/conduit/method/x/
/conduit/method/user.whoami/
/conduit/log/

Reviewers: btrahan, epriestley

Reviewed By: epriestley

CC: aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2326
Use a disk-based default avatar, not a database-based one

Summary:
This is mostly in an effort to simplify D2323. Currently, we load one image into the database by default. This is a weird special case that makes things more complicated than necessary.

Instead, use a disk-based default avatar.

Test Plan: Verified that a user without an image appears with the default avatar as a handle, in profile settings, and on their person page.

Reviewers: btrahan, vrana, edward, jungejason

Reviewed By: vrana

CC: aran

Maniphest Tasks: T345

Differential Revision: https://secure.phabricator.com/D2331
Hard-code and unify "more applications" in Phabricator

Summary:
This is mostly intended to simplify D2323.

We currently allow users to edit and customize the links on the homepage, but as far as I know no one actually does this (no one complained when we redid the homepage earlier this year) and it creates a lot of mess in the database patches and quickstart dump. After D2331, this is the only data we load in the patch files. The patch files are also a mess with respect to this data and have various different versions of it.

Also the current UI is just kind of bad, it stretches stuff across too many screens and is generally ungood. Nuking this lets us nuke a lot of code in general.

(In the long term, I think we'll move toward an "application" model anyway, and this stuff will go away sooner or later.)

I'll add a drop-database patch some time later, just in case anyone does actually use this, so they can get their data out of MySQL.

Test Plan: Looked at home page, clicked "More Stuff", got a single list of other apps/things.

Reviewers: btrahan, vrana, edward, jungejason

Reviewed By: jungejason

CC: aran

Maniphest Tasks: T345

Differential Revision: https://secure.phabricator.com/D2332
Don't fatal on image macro list if a file has been deleted

Summary:
We added the ability to delete files a while ago, but this interface isn't happy about it.

I still render the macro so you can see/delete it, e.g.

Test Plan: Viewed a deleted macro page, got a page instead of an error. Also verified that the actual remarkup part doesn't have issues.

Reviewers: btrahan, vrana, jungejason

Reviewed By: jungejason

CC: aran

Differential Revision: https://secure.phabricator.com/D2328
Minor, fix access log issue with non-auth methods.
Clarify "Closed" revision status with VCS-specific language

Summary: Instead of rendering "Revision Status: Closed (Sat, Apr 28, 10:28 AM)", render "Revision Status: Closed (Pushed Sat, Apr 28, 10:28 AM)", or "Committed", as appropriate.

Test Plan: Looked at a committed revision.

Reviewers: btrahan, vrana, jungejason

Reviewed By: jungejason

CC: jeffmo, rdbayer, aran

Maniphest Tasks: T909

Differential Revision: https://secure.phabricator.com/D2334
Minor, fix an error when looking at a new, unparsed repository.
Add "jump to table of content" keyboard shortcut

Summary:
Many times when I'm reading a big diff, I want to go to the
TOC. Add it.

Test Plan:
can navigate with 't'. It also shows up in '?'

Revert Plan:

Reviewers: epriestley, vrana

Reviewed By: epriestley

CC: nh, aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2335
Detect copied code by own algorithm

Summary:
Required for D2321.
Deprecates D2320.
Uses algorithm described at D2320#16.

Complexity of this algorithm would be `O(N)` (`N` stands for number of lines) in most cases.
The worst case is `O(A*F)` (`A` stands for number of added lines, `F` for number of colliding lines) but it should be pretty rare. Real-world example is 100 modified files with moved license block (15 lines) in each. This will require 1500*100 comparisons because the algorithm will be trying to find the longest block in each file.

Test Plan:
`arc diff --only` on commit with copied code.
More tests on standalone algorithm.

Reviewers: epriestley

Reviewed By: epriestley

CC: aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2333
Highlight copied/moved lines in Differential

Summary: The color used for this feature is pretty important and I am bad with colors.

Test Plan:
View diff created by D2320 with some copied lines and one line changed:

{F10604, size=full}

Reviewers: epriestley

Reviewed By: epriestley

CC: aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2321
Fix typos in detectCopiedCode()

Auditors: epriestley
Show README on repository screen in Diffusion

Summary:
  - Show README on the repository screen.
  - Move README to the bottom of the page for both repository and browse screens.
  - Support "README.rainbow".

Test Plan: Looked at repository, browse screens. Made a "README.rainbow".

Reviewers: btrahan, vrana, jungejason

Reviewed By: btrahan

CC: aran

Maniphest Tasks: T1104

Differential Revision: https://secure.phabricator.com/D2336
SQL Patch Management: SQL Changes

Summary:
Splits out the SQL changes. These are most of the changes, but primarily mechanical:

  - Moved "initialize.sql" to "0000.legacy.sql" and partially reverted to an older version, such that patches 0000 + 000 + 001 + ... + 137 put us in the right state when applied sequentially.
  - Removed "create database" commands from all SQL. These are handled by separate DB patches now, so we have the data to do operations like "storage databases" (list databases) and "storage destroy" (drop databases).
  - Removed "phabricator_" namespace from all SQL, and replaced with "{$NAMESPACE}_" token so we can namespace databases.
  - Shortened some column lengths so patches apply correctly if originally created as InnoDB; also a few similar tweaks elsewhere.

Test Plan: See D2323 for discussion and test plan.

Reviewers: edward, vrana, btrahan, jungejason

Reviewed By: btrahan

CC: aran

Maniphest Tasks: T140, T345

Differential Revision: https://secure.phabricator.com/D2329
Make SQL patch management DAG-based and provide namespace support

Summary:
This addresses three issues with the current patch management system:

  # Two people developing at the same time often pick the same SQL patch number, and then have to go rename it. The system catches this, but it's silly.
  # Second/third-party developers can't use the same system to manage auxiliary storage they may want to add.
  # There's no way to build mock databases for unit tests that need to do reads.

To resolve these things, you can now name your patches whatever you want and conflicts are just merge conflicts, which are less of a pain to fix than filename conflicts.

Dependencies are now a DAG, with implicit dependencies created on the prior patch if no dependencies are specified. Developers can add new concrete subclasses of `PhabricatorSQLPatchList` to add storage management, and define the dependency branchpoint of their patches so they apply in the correct order (although, generally, they should not depend on the mainline patches, presumably).

The commands `storage upgrade --namespace test1234` and `storage destroy --namespace test1234` will allow unit tests to build and destroy MySQL storage.

A "quickstart" mode allows an upgrade from scratch in ~1200ms. Destruction takes about 200ms. These seem like fairily reasonable costs to actually use in tests. Building from scratch patch-by-patch takes about 6000ms.

Test Plan:
  - Created new databases from scratch with and without quickstart in a separate test namespace. Pointed the webapp at the test namespaces, browsed around, everything looked good.
  - Compared quickstart and no-quickstart dump states, they're identical except for mysqldump timestamps and a few similar things.
  - Upgraded a legacy database to the new storage format.
  - Destroyed / dumped storage.

Reviewers: edward, vrana, btrahan, jungejason

Reviewed By: btrahan

CC: aran, nh

Maniphest Tasks: T140, T345

Differential Revision: https://secure.phabricator.com/D2323
Inform about moved code and prefer it over copied code

Summary:
Also reduce the memory usage a little bit (before increasing it again).

I use the same CSS class as for the copied code.

Test Plan: Parsed 100 diffs and checked about 10 of them - looks good.

Reviewers: epriestley

Reviewed By: epriestley

CC: aran, Koolvin

Differential Revision: https://secure.phabricator.com/D2339
Ignore non-existing diffs in copied code detector script

Auditors: epriestley