bugfix: lib/common.Makefile: `svn add`: need to run with --force because the new version of svn in the latest Mac upgrade errors if the file is already under version control

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

lib/common.Makefile: added %/live, for use with `make inputs/download`

Makefile, schemas/.Mac.conf: upgraded to PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality. this also removes the Mac 10.8 Mountain Lion quirks, such as renaming the postgres user to _postgres (which messed everything up, but is now back to normal).

bugfix: lib/common.Makefile: $(subMake): don't enclose the target in "" because sometimes the target is empty (i.e. `all`), and nothing should be passed to the sub-make

bugfix: *Makefile: recursive invocation of $(MAKE): enclose targets in "" in case they contain *

bugfix: schemas/Makefile, lib/common.Makefile: enclose schema names in "" so that they won't be lowercased

bugfix: lib/common.Makefile: $(asAdmin): need to use _postgres instead on Mac for OS X 10.8 Mountain Lion

bugfix: *Makefile: $(asAdmin) invocations of Postgres commands: need to set DB user to postgres so that it won't default to the system user _postgres

lib/common.Makefile: added $(psqlOpts), $(psqlAsAdmin)

lib/common.Makefile: added $(asAdmin)

bugfix: lib/common.Makefile: gzip/gunzip: in `touch -r`, $< needs to be the reference file

/Makefile: moved %/remake, %-remake to lib/common.Makefile because they are generally useful

/Makefile: moved %/reinstall to lib/common.Makefile because it is generally useful

bugfix: lib/common.Makefile: Compression: %.gz <-> %: only run command if target does not exist, to avoid overwriting the target when the compressed or uncompressed version is newer than it. the difference in mtimes can arise when one file is created after the other, and should not cause the opposite operation to be performed to try to make the other file up-to-date (leading to an infinite back-and-forth of creating one file from the other).

lib/common.Makefile: Added $(require_var)

lib/common.Makefile: Compression: Added `%:: .gz`, `.gz: %`

lib/common.Makefile: rsync: $(rsync): Also exclude .lk* lock files

lib/common.Makefile: rsync: $(rsync*): Use --no-group because the file group is different depending on the machine

lib/common.Makefile: remote server: Use jupiter instead of vegbiendev, to ensure that all files get uploaded there rather than only to vegbiendev. This involves adding an extra database import step to download the uploaded files from jupiter onto vegbiendev.

Moved Checksums from backups/Makefile to lib/common.Makefile so all dirs (including inputs/) can use md5sum testing

lib/common.Makefile: $(remote): Made remote basepath configurable in $(remote_basepath)

lib/common.Makefile: Renamed $(src_server) to $(remote_host) and $(src_user) to $(remote_user) for clarity

lib/common.Makefile: Added $(ucase) and $(ci)

lib/common.Makefile: Added $(mkdir)

lib/common.Makefile: $(subMake): Removed `--makefile=../input.Makefile`, which is specific just to inputs/Makefile

Makefiles: Changed "Usage: `make -s ...`" to "Run with `make -s` to avoid echoing make commands"

lib/common.Makefile: Added $(and), $(or), $(not)

lib/common.Makefile: $(confirm): Added comment that this requires `SHELL := /bin/bash` to work correctly

lib/common.Makefile: System: Added $(mtime)

lib/common.Makefile: $(date): Factored date format out into $(dateFmt)

backups/Makefile: Factored $(isMac) out into lib/common.Makefile

lib/common.Makefile: Added version target, which prints the current $(version) value

lib/common.Makefile: Revisions: $(version): Use just the revision # to avoid cluttering the schema and log file names with long datetime strings

lib/common.Makefile: Replaced no longer used $(date) with function to generate human-readable text date (rather than date to put in filename). Removed leading zeros from date and hour. Added timezone.

Makefiles: Factored out common vars/functions into lib/common.Makefile

lib/common.Makefile: Revisions: Allow $(version) to be overridden in the environment, so that the public schema and all log files share the same, pregenerated version

lib/common.Makefile: SVN: $(add*): Fixed bug where need to use --depth=empty to ensure directory contents are not added unless explicitly listed

lib/common.Makefile: Filesystem: $(wildcard/): Fixed bug where {} exprs weren't handled correctly when some branches contained *, by using `shopt -s nullglob` and bash directly instead of trying to emulate it with grep

lib/common.Makefile: SVN: Added $(add*)

lib/common.Makefile: rsync: $(rsync): Exclude .svn, #, and .DS_Store rather than all . because dirs beginning with . created by the user (such as .NCBI, .TNRS) should be included in the sync

lib/common.Makefile: Added $(comma)

lib/common.Makefile: $(version): Include both the svn revision when make was started as well as the svn revision when the command is actually run (when these values differ), in case svn was updated between the time an import was started and the time a particular table started being imported. Because tables within a datasource are imported sequentially, it is possible that an update would have happened before the last table started importing.

Factored OS section out from Makefile, input.Makefile into lib/common.Makefile

lib/common.Makefile: Added $(version), to replace $(date) for versioning log files, etc., and helper function $(rootRevision)

lib/common.Makefile: Added $(revision)

lib/common.Makefile: Added $(sed)

Factored $(date) out from Makefile, input.Makefile into lib/common.Makefile

lib/common.Makefile: rsync: Added $(rsync*) to rsync all files, including those starting with "."

lib/common.Makefile: Added $(+w)

lib/common.Makefile: Added $(no/) to remove trailing /

lib/common.Makefile: SVN: Added $(addFile)

lib/common.Makefile: Added $(wildcard/) (needed because builtin $(wildcard) doesn't do / suffix correctly)

lib/common.Makefile: Added $(cp)

lib/common.Makefile: Added $(CP)

lib/common.Makefile: Added empty clean target to make sure `make clean` always works

lib/common.Makefile: Added vars for chars not allowed in make targets. Added functions/vars to replace "_" with " ".

lib/common.Makefile: rsync: Time the rsync operation

lib/common.Makefile: rsync: $(remote): Fixed bug where the inputs/ dir was hardcoded, when the remote dir name needed to be determined dynamically based on the Makefile dir

Moved generally useful targets and vars from inputs/Makefile to lib/common.Makefile and lib/forwarding.Makefile