lib/sh/make.sh: make(): added support for $output_data mode which uses --silent

fix: lib/sh/util.sh: already_exists_msg(): changed calling convention to avoid it seeming like `return 0` is run if already_exists_msg() throws an error, when in fact already_exists_msg() is just a command that should be run before returning/errexiting

fix: inputs/input.Makefile: need to escape $ in commands, including inside comments

bugfix: lib/common.Makefile: $(wildcard/): need final pass with $(wildcard) to support inputs without wildcard chars

bugfix: inputs/input.Makefile: `$(call add*,$(svnFiles))` must be invoked externally to clear the $(wildcard) cache before expanding $(svnFiles)

/README.TXT: Installation: added instructions for inputs/download/live prompts

/README.TXT: Installation: added instructions for MySQL installation prompts

fix: /README.TXT: Installation: "Are you sure you want to continue connecting" prompt comes before "aaronmk@jupiter's password" prompt

/Makefile: phppgadmin-Linux: removed no longer needed $(editApacheConfForPhppgadmin), as phpPgAdmin no longer uses this file (/etc/phppgadmin/apache.conf)

/Makefile: phppgadmin-Linux: removed no longer needed $(editPhppgadminApacheConf)

/Makefile: misc-Linux: added htop

/Makefile: misc-Linux: added jedit

/Makefile: postgres-Linux: added pgadmin3

bugfix: /Makefile: $(postgresReload-*) calls: do not prepend $(MAKE) or - because these are multi-command functions

bugfix: /Makefile: $(bien*Password): need to use = instead of := because these files are not available until config/download/live has run

fix: /README.TXT: Installation: added instructions for "aaronmk@jupiter's password" prompt

/README.TXT: Installation: added step to open a terminal window

fix: /README.TXT: Installation: added instructions for "Are you sure you want to continue connecting" prompt

inputs/VegBank/run*.log: updated. this adds the function call context in addition to the function location.

bugfix: /Makefile: $(uutils_install): need to exit after printing instructions instead of continuing

fix: /README.TXT: Installation: need instructions for "reload PATH" prompt

fix: /README.TXT: Installation: `apt-get install subversion`: need --yes

bugfix: /Makefile: bin/install: uutils: need to reopen terminal window before can proceed with other installation steps

/Makefile: python-Linux: removed no longer used installation of pp (Parallel Python). we use Python's multiprocessing package instead.

bugfix: /Makefile: install: must be config/download/live, not config/download

README.TXT: bin/sync_upload calls as root: don't need to set $USER because this is now set to the correct value in bin/sync_upload's scripts

bugfix: lib/sh/local.sh: $sync_remote_url: jupiter user is always aaronmk, not the local user

*{.sh,run}: use standard WARNING syntax for warning labels

bugfix: /Makefile: bin/install: also need to install uutils

*{.sh,run}: use standard WARNING syntax for warning labels

fix: lib/sh/util.sh: verbosity_compat(): documented that this should not be run until right before executing an external command, so that it doesn't mess up the logging mechanism

bugfix: bin/make: don't run verbosity_compat until right before executing the external command, so that it doesn't mess up the logging mechanism. this is run automatically by command(), so there is no need to do anything here. note that logging bugs like these can now be troubleshooted much more easily with pst() to narrow down which functions could be causing the problem.

bugfix: lib/sh/util.sh: functions called by pst(): commented out/removed logging calls that would have caused infinite recursion when pst()'ing a logging function

lib/sh/util.sh: echo_func(): get call context before wrapper(s), which is more useful for debugging. this uses skip_stack_frames()'s lookahead=1 mode.

fix: lib/sh/util.sh: skip_stack_frames() callers: updated for new skip_stack_frames rather than get_stack_frame behavior

lib/sh/util.sh: skip_stack_frames(): added lookahead support, which looks at entry after current to deterine whether to skip current. this is useful for skipping wrappers, by looking at the calling function's name.

fix: lib/sh/util.sh: skip_stack_frames(): for new skip_stack_frames rather than get_stack_frame behavior, stack frames must be skipped in the caller to preserve the stack frame pointer

lib/sh/util.sh: get_stack_frame_after(): renamed to skip_stack_frames() for clarity

lib/sh/util.sh: added skip_stack_frame_in_caller, unskip_stack_frame_in_caller

lib/sh/util.sh: added prev_stack_frame

lib/sh/util.sh: echo_func(): use new format_stack_frame, which adds call context information to what was provided by func_loc

fix: lib/sh/util.sh: format_stack_frame(): need to hide canon_rel_path() info using log+

lib/sh/util.sh: added get_stack_frame_after()

lib/sh/util.sh: added matches()

lib/sh/util.sh: next_stack_frame: documented usage

fix: lib/runscripts/util.run: runscript template: all(): moved example commands to target(), where they would more likely be located

lib/sh/util.sh: format_stack_frame(): support including args

lib/sh/util.sh: debugging: added pst() (print_stack_trace)

lib/sh/util.sh: added stack_trace(), print_stack_trace()

lib/sh/util.sh: added format_stack_frame()

lib/sh/util.sh: added get_stack_frame() and helpers

lib/sh/util.sh: terminal: moved before errors so it can be used by it

lib/sh/util.sh: errors, debugging: moved after datatype sections so their functions can use these

bugfix: lib/sh/util.sh: canon_rel_path() stub: proper no-op requires passing through original path

lib/sh/util.sh: canon_rel_path(): fall back to original path if can't resolve, instead of errexiting

bugfix: lib/sh/util.sh: canon_rel_path(): don't re-localize $path because this clears it

lib/sh/util.sh: canon_rel_path(): import $1 to $path before function body, so that the function body can be moved to a nested function

lib/sh/util.sh: added canon_rel_path() stub for use by debugging functions

bugfix: /Makefile: install: run bin/install first since config/download depends on it

lib/sh/util.sh: moved func_loc() to before debugging section so it can be used by debugging functions

bugfix: lib/sh/util.sh: command__exec(): need to restore $verbosity before calling die_e

bugfix: /Makefile: install: also need to run config/download to get the necessary passwords

config/Makefile: added download target

/Makefile: config: renamed to bin/install because config is the name of a directory

/README.TXT: Installation: `make install`: added instructions for what to do at each prompt

/README.TXT: Installation: Check out svn: need to install svn first as this does not come preinstalled on Ubuntu

fix: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: make(): added warning that this will truncate the geoscrub database tables

/README.TXT: to back up the local machine's hard drive: just do a single pass, to avoid the numerous different steps

backups/*retention_policy*: on jupiter: changed to avoid retaining backups further back, as these consume significant disk space on jupiter and are not useful for anything

fix: lib/sh/local.sh: $sync_remote_url: need $USER so user can be overridden when running as root

fix: /README.TXT: to back up the local machine's settings: to jupiter: need `sudo -E` for new Documents/BIEN/vegbiendev*/

/README.TXT: backups of ~/.dropbox/: just pause and resume Dropbox instead of quitting and restarting it

/README.TXT: to back up the local machine's settings: to Dropbox: exclude gmvault-db/ to save space in Dropbox

/README.TXT: to back up the local machine's settings: don't need to exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because the disk that was corrupting this file has been replaced (#907)

/README.TXT: to back up e-mails: don't need to also sync aaronmk@nceas.ucsb.edu because these e-mails are also in aaronmk.nceas@gmail.com (auto-forwarded)

/README.TXT: Notes on system stability: removed no longer applicable warning about system upgrades, which is now incorrect because the disk space overrun bug (#887) was found not to have been caused by a system upgrade

web/links/index.htm: updated to Firefox bookmarks: Roundtable: added links for Roundtable on "obstacles faced by researchers who reuse, share and manage data, and strategies for overcoming them"

lib/Firefox_bookmarks.reformat.csv: label page's self-description as such: also support quotations enclosed in '

fix: exports/native_status_resolver.csv.run: added `users_by_name=1` to preserve the file group

added inputs/VegBank/run.call_graph.log

inputs/VegBank/run.log: updated for echo_vars() changes. the PG* vars, which contain important information, will now not need to be filtered out.

lib/sh/util.sh: echo_vars(): merge repeated flags so there aren't flags in between the vars (which is also not valid declare syntax)

lib/sh/db.sh: pg_cmd(): log vars on same line to avoid clutter

lib/sh/util.sh: echo_vars(): put all the vars on the same line so they don't clutter up the call graph generated at the default verbosity

web/links/index.htm: updated to Firefox bookmarks: Mac: added link for VNC client. extended attributes: added link for chflags.

added planning/workflow/staging_tables_installation_for_SQL_datasource.odg.src.log

added inputs/VegBank/run.log

fix: inputs/input.Makefile: $(svnFilesGlob): *.log should be in both the subdirs and the main dir

inputs/input.Makefile: $(svnFilesGlob): *.log

inputs/Makefile: install: install an empty VegBIEN schema instead of all the datasources, at Mark's request. this enables loading just a single datasource.

schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated

bugfix: schemas/public_.sql: view_full_occurrence_individual_view and related views: synced to data dictionary spreadsheet, which adds back the links to the definitions (which used to be part of the column name itself)

fix: schemas/public_.sql: analytical_plot, analytical_specimen: updated column names to be the same as analytical_stem, which these are a subset of

/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: avoid extraneous diffs when rsyncing: clarified the machines that the command should be run on

web/links/index.htm: updated to Firefox bookmarks: removed broken favicons

web/links/index.htm: updated to Firefox bookmarks: updated favicons

fix: /README.TXT: to backup files not in Time Machine: need to use 2 TB external hard drive instead of Time Machine drive because Time Machine drive does not have ~/Documents/BIEN/ in a location where it can be hardlinked against

web/links/index.htm: updated to Firefox bookmarks: categorized uncategorized bookmarks

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/links/index.htm: updated to Firefox bookmarks: local machine phpPgAdmin: removed this so the Mac won't get woken up on network access whenever someone opens the links page, which attempts to load the favicon from the local machine. the previous solution of manually deleting the favicon (r13406) doesn't work because the favicon will just get re-added whenever this bookmark is visited.