{"thread":{"id":"53384","subject":"file is showing as modified even that it was never commited","startedAt":"2020-05-03T20:03:29Z","lastAt":"2020-05-05T08:34:17Z","messageCount":17,"participants":["Ewa Śliwińska","Shourya Shukla","Sergey Organov","Andreas Schwab"],"isPatch":false,"patchVersion":null,"patchTotal":null},"messages":[{"id":"396881","messageId":"CAEoQP9iY-0+=ETA0vrHL0HngccwtNA_3KX4WSSokJpOgJDGUeA@mail.gmail.com","threadId":"53384","inReplyTo":"CAEoQP9gVur=UDDPzHnLq-AryDnd45uYdEs3kajzLrtr572e_rA@mail.gmail.com","subject":"file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-03T20:03:15Z","receivedAt":"2020-05-03T20:03:29Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"Hi,\n\nI’m probably missing something here, but it looks really weird and I\ncan’t find any information on this.\n\nMy situation is as following:\nI created empty repository on Bitbucket, then cloned it, added code\nand made one initial commit (without push).\n\nNow I changed the code and I would like to commit it, but I have some troubles.\n\nThe problem is some files are showing as changed while I never committed them.\nI never intended to commit them (they are under .idea directory, which\nI added to .gitignore).\nI checked with git log - I have only this one commit.\nI checked files affected by this commit using git show --pretty=\"\"\n--name-only. Mentioned files are not there.\nAlso checked the history of one particular file, using git log -p - no\nhistory here.|\n\nAt the same time, file is showing is changes not staged for commit\nwhen calling git status.\nFor what is worth, file is even not there.\n\nI hope you’ll help me unravel this. I am out of ideas, kind of seems like a bug.\n\nBest regards\nEwa\n"},{"id":"396887","messageId":"20200504055530.GA13290@konoha","threadId":"53384","inReplyTo":"CAEoQP9iY-0+=ETA0vrHL0HngccwtNA_3KX4WSSokJpOgJDGUeA@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Shourya Shukla","fromEmail":"shouryashukla.oo@gmail.com","sentAt":"2020-05-04T05:55:30Z","receivedAt":"2020-05-04T05:55:39Z","isPatch":false,"sender":{"key":"shouryashukla.oo@gmail.com","avatar":"https://avatars.githubusercontent.com/u/43680618?v=4"},"body":"Hey Ewa!\n\nThis might be the fix for you:\n\nA `gitignore` file ensures that certain file(s) which are not\ntracked by Git remain untracked. However, sometimes particular\nfile(s) may have been tracked before adding them into the\n`.gitignore`, hence they still remain tracked. To untrack and\nignore files/patterns, use `git rm --cached `\nand add a pattern to `.gitignore` that matches the .\n\nMost probably the '.idea' folder might have been tracked before adding\nit to the '.gitignore' and hence it shows up in the staging area (i.e.,\nwhen you run a `git status`, it shows up as modified).\n\nIf there is a doubt still, feel free to drop a message here :)\n\nRegards,\nShourya Shukla\n\n"},{"id":"396891","messageId":"CAEoQP9g2UKQDi0i8Fi4HRp1d_U=qq4gfoK_vGwRYuPN+mU+GxQ@mail.gmail.com","threadId":"53384","inReplyTo":"20200504055530.GA13290@konoha","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-04T08:17:57Z","receivedAt":"2020-05-04T08:18:09Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"Hi,\n\nthanks for your response.\nI consider what you propose rather a workaround, while it is really\nimportant for me to get to know what happened here.\nCould you help me investigate this?\n\nI though that I might add those files accidentally before. That's why\nI checked it, I described it in the original email.\nDid I check in a wrong way?\n"},{"id":"396894","messageId":"20200504120024.GA3372@konoha","threadId":"53384","inReplyTo":"CAEoQP9hyMi=oj18atTJo+dR3ve_zzrLQoOja0CKAAVHei6rA0g@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Shourya Shukla","fromEmail":"shouryashukla.oo@gmail.com","sentAt":"2020-05-04T12:00:24Z","receivedAt":"2020-05-04T12:00:34Z","isPatch":false,"sender":{"key":"shouryashukla.oo@gmail.com","avatar":"https://avatars.githubusercontent.com/u/43680618?v=4"},"body":"On 04/05 10:11, Ewa Śliwińska wrote:\n> Hi,\n> \n> thanks for your response.\n> I consider what you propose rather a workaround, while it is really\n> important for me to get to know what happened here.\n> Could you help me investigate this?\n\nThat actually was a solution to your problem, not a workaround.\n\n> I though that I might add those files accidentally before. That's why I\n> checked it, I wrote about this in the original email.\n> Did I check in a wrong way?\n\nIf we go into detail of what might have actually happened, the `.idea`\nfolder must've been tracked before getting a mention in the\n`.gitignore`. Now, the thing is that `.gitignore` ignores only those\npatterns/files which were not tracked since their addition in it. So\nmost probably, this would have been the case with `.idea` as well.\n\nAnd yes, you might have added those files before accidentally, maybe\nwhen you did a `git add .` or something alike.\n\nRegards,\nShourya Shukla\n"},{"id":"396895","messageId":"CAEoQP9gs-a1NanNpYiFQgTs0C+CeYhbD8rMjoFVat1ZSijNA2A@mail.gmail.com","threadId":"53384","inReplyTo":"20200504120024.GA3372@konoha","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-04T12:11:15Z","receivedAt":"2020-05-04T12:11:29Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"> That actually was a solution to your problem, not a workaround.\nNot really, because I would like to investigate what happened, not\njust fix it. In that case I could as well recreate repository I\nguess...\n\nI agree that I could add those files accidentally. But I'm really\ndisappointed in fact that you seem to ignore all the part where I\ndescribed in details how I checked this and why I think this is not\nthe case.\nCould you please answer if there was something wrong with my checking?\nI'm asking second time.\n\nOr could you guide me step by step through investigation which would\nconfirm your theory?\n\nOn Mon, 4 May 2020 at 14:00, Shourya Shukla wrote:\n>\n> On 04/05 10:11, Ewa Śliwińska wrote:\n> > Hi,\n> >\n> > thanks for your response.\n> > I consider what you propose rather a workaround, while it is really\n> > important for me to get to know what happened here.\n> > Could you help me investigate this?\n>\n> That actually was a solution to your problem, not a workaround.\n>\n> > I though that I might add those files accidentally before. That's why I\n> > checked it, I wrote about this in the original email.\n> > Did I check in a wrong way?\n>\n> If we go into detail of what might have actually happened, the `.idea`\n> folder must've been tracked before getting a mention in the\n> `.gitignore`. Now, the thing is that `.gitignore` ignores only those\n> patterns/files which were not tracked since their addition in it. So\n> most probably, this would have been the case with `.idea` as well.\n>\n> And yes, you might have added those files before accidentally, maybe\n> when you did a `git add .` or something alike.\n>\n> Regards,\n> Shourya Shukla\nPozdrawiam\nEwa\n\nOn Mon, 4 May 2020 at 14:00, Shourya Shukla wrote:\n>\n> On 04/05 10:11, Ewa Śliwińska wrote:\n> > Hi,\n> >\n> > thanks for your response.\n> > I consider what you propose rather a workaround, while it is really\n> > important for me to get to know what happened here.\n> > Could you help me investigate this?\n>\n> That actually was a solution to your problem, not a workaround.\n>\n> > I though that I might add those files accidentally before. That's why I\n> > checked it, I wrote about this in the original email.\n> > Did I check in a wrong way?\n>\n> If we go into detail of what might have actually happened, the `.idea`\n> folder must've been tracked before getting a mention in the\n> `.gitignore`. Now, the thing is that `.gitignore` ignores only those\n> patterns/files which were not tracked since their addition in it. So\n> most probably, this would have been the case with `.idea` as well.\n>\n> And yes, you might have added those files before accidentally, maybe\n> when you did a `git add .` or something alike.\n>\n> Regards,\n> Shourya Shukla\n"},{"id":"396936","messageId":"874ksvei1r.fsf@osv.gnss.ru","threadId":"53384","inReplyTo":"CAEoQP9gs-a1NanNpYiFQgTs0C+CeYhbD8rMjoFVat1ZSijNA2A@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Sergey Organov","fromEmail":"sorganov@gmail.com","sentAt":"2020-05-04T17:17:20Z","receivedAt":"2020-05-04T17:17:27Z","isPatch":false,"sender":{"key":"sorganov@gmail.com","avatar":"https://avatars.githubusercontent.com/u/8501568?v=4"},"body":"Dear Ewa,\n\nPlease see below.\n\nEwa Śliwińska writes:\n\n>> That actually was a solution to your problem, not a workaround.\n\n> Not really, because I would like to investigate what happened, not\n> just fix it. In that case I could as well recreate repository I\n> guess...\n>\n> I agree that I could add those files accidentally. But I'm really\n> disappointed in fact that you seem to ignore all the part where I\n> described in details how I checked this and why I think this is not\n> the case.\n\nExcept you didn't give actual details. Please give exact commands you\nissued and exact answers you've got.\n\nFor example:\n\n$ ls .test\na x\n$ git status\nOn branch v4.0\nYour branch and 'origin/v4.0' have diverged,\nand have 2 and 29 different commits each, respectively.\n (use \"git pull\" to merge the remote branch into yours)\n\nChanges not staged for commit:\n (use \"git add ...\" to update what will be committed)\n (use \"git checkout -- ...\" to discard changes in working directory)\n\n\tmodified: .test/a\n\nno changes added to commit (use \"git add\" and/or \"git commit -a\")\n$ git log -- .test\ncommit e1e7818f4120b5ebc622c8dbf1b257ea8a03530c\nAuthor: Sergey Organov \nDate: Mon May 4 18:55:58 2020 +0300\n\n Test\n\n$ git log -- .test/a\ncommit e1e7818f4120b5ebc622c8dbf1b257ea8a03530c\nAuthor: Sergey Organov \nDate: Mon May 4 18:55:58 2020 +0300\n\n Test\n$ git log -- .test/x\n$ \n\n> Could you please answer if there was something wrong with my checking?\n\nNobody could tell unless you actually show us your checkings.\n\n> I'm asking second time.\n\nThanks, we've noticed.\n\n-- Sergey\n"},{"id":"396952","messageId":"CAEoQP9guAWg8E95Pi4MOih7z5rPg7OCB+_jZ6EMhJxpFsM3A1A@mail.gmail.com","threadId":"53384","inReplyTo":"874ksvei1r.fsf@osv.gnss.ru","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-04T18:39:10Z","receivedAt":"2020-05-04T18:39:24Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"Hi Sergey,\n\nThanks for engaging here.\n\nActually, I gave some details in the first email, I'm not sure if they\nwere even noticed.\n\nAbout asking second time: I emphasized this because I felt this part\nwas ignored and I didn't like it.\n\nI wanted to describe problem more generally and gave you the commands.\nBut now I will paste the console full output as you demanded:\n\nmac:lp3rater noelo$ git status\n\nOn branch master\n\nYour branch is based on 'origin/master', but the upstream is gone.\n\n (use \"git branch --unset-upstream\" to fixup)\n\n\nChanges to be committed:\n\n (use \"git reset HEAD ...\" to unstage)\n\n\nnew file: .idea/.gitignore\n\nnew file: .idea/compiler.xml\n\nnew file: .idea/encodings.xml\n\nnew file: .idea/jarRepositories.xml\n\nnew file: .idea/libraries/Maven__commons_codec_commons_codec_1_11.xml\n\nnew file: .idea/libraries/Maven__commons_io_commons_io_2_6.xml\n\nnew file: .idea/libraries/Maven__commons_logging_commons_logging_1_2.xml\n\nnew file: .idea/libraries/Maven__commons_net_commons_net_3_6.xml\n\nnew file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_2_39_1.xml\n\nnew file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_core_js_2_39_0.xml\n\nnew file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_cssparser_1_5_0.xml\n\nnew file: .idea/libraries/Maven__net_sourceforge_htmlunit_neko_htmlunit_2_39_0.xml\n\nnew file: .idea/libraries/Maven__org_apache_commons_commons_lang3_3_10.xml\n\nnew file: .idea/libraries/Maven__org_apache_commons_commons_text_1_8.xml\n\nnew file: .idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_5_12.xml\n\nnew file: .idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_4_13.xml\n\nnew file: .idea/libraries/Maven__org_apache_httpcomponents_httpmime_4_5_12.xml\n\nnew file: .idea/libraries/Maven__org_brotli_dec_0_1_2.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_jetty_client_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_jetty_http_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_jetty_io_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_jetty_util_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_jetty_xml_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_api_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_client_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_common_9_4_27_v20200227.xml\n\nnew file: .idea/libraries/Maven__xalan_serializer_2_7_2.xml\n\nnew file: .idea/libraries/Maven__xalan_xalan_2_7_2.xml\n\nnew file: .idea/libraries/Maven__xerces_xercesImpl_2_12_0.xml\n\nnew file: .idea/libraries/Maven__xml_apis_xml_apis_1_4_01.xml\n\nnew file: .idea/misc.xml\n\nnew file: .idea/modules.xml\n\nnew file: .idea/sonarlint/issuestore/2/2/22a598feccb13c958ecc8eff5c53a9a7f9470a72\n\nnew file: .idea/sonarlint/issuestore/4/4/442292b8a7efeabbe4cc176709b833b1792140ec\n\nnew file: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n\nnew file: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n\nnew file: .idea/sonarlint/issuestore/index.pb\n\nnew file: .idea/vcs.xml\n\n\nChanges not staged for commit:\n\n (use \"git add ...\" to update what will be committed)\n\n (use \"git checkout -- ...\" to discard changes in working directory)\n\n\nmodified: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n\nmodified: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n\nmodified: .idea/sonarlint/issuestore/index.pb\n\nmodified: src/main/java/Downloader.java\n\nmac:lp3rater noelo$ git log\n\ncommit 50001426b28ed80433484f24831c160fcf15eec1 (HEAD -> master)\n\nAuthor: Ewa Śliwiska \n\nDate: Fri May 1 22:02:10 2020 +0200\n\n\n content of the main page displayed\n\nmac:lp3rater noelo$ git show --pretty=\"\" --name-only 5000142\n\n.gitignore\n\npom.xml\n\nsrc/main/java/Application.java\n\nsrc/main/java/Downloader.java\n\nmac:lp3rater noelo$ git log -p\n.idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n\nmac:lp3rater noelo$\n\nBest regards\nEwa\n\nOn Mon, 4 May 2020 at 19:17, Sergey Organov wrote:\n>\n> Dear Ewa,\n>\n> Please see below.\n>\n> Ewa Śliwińska writes:\n>\n> >> That actually was a solution to your problem, not a workaround.\n>\n> > Not really, because I would like to investigate what happened, not\n> > just fix it. In that case I could as well recreate repository I\n> > guess...\n> >\n> > I agree that I could add those files accidentally. But I'm really\n> > disappointed in fact that you seem to ignore all the part where I\n> > described in details how I checked this and why I think this is not\n> > the case.\n>\n> Except you didn't give actual details. Please give exact commands you\n> issued and exact answers you've got.\n>\n> For example:\n>\n> $ ls .test\n> a x\n> $ git status\n> On branch v4.0\n> Your branch and 'origin/v4.0' have diverged,\n> and have 2 and 29 different commits each, respectively.\n> (use \"git pull\" to merge the remote branch into yours)\n>\n> Changes not staged for commit:\n> (use \"git add ...\" to update what will be committed)\n> (use \"git checkout -- ...\" to discard changes in working directory)\n>\n> modified: .test/a\n>\n> no changes added to commit (use \"git add\" and/or \"git commit -a\")\n> $ git log -- .test\n> commit e1e7818f4120b5ebc622c8dbf1b257ea8a03530c\n> Author: Sergey Organov \n> Date: Mon May 4 18:55:58 2020 +0300\n>\n> Test\n>\n> $ git log -- .test/a\n> commit e1e7818f4120b5ebc622c8dbf1b257ea8a03530c\n> Author: Sergey Organov \n> Date: Mon May 4 18:55:58 2020 +0300\n>\n> Test\n> $ git log -- .test/x\n> $\n>\n> > Could you please answer if there was something wrong with my checking?\n>\n> Nobody could tell unless you actually show us your checkings.\n>\n> > I'm asking second time.\n>\n> Thanks, we've noticed.\n>\n> -- Sergey\n"},{"id":"396976","messageId":"87o8r3cwcn.fsf@osv.gnss.ru","threadId":"53384","inReplyTo":"CAEoQP9guAWg8E95Pi4MOih7z5rPg7OCB+_jZ6EMhJxpFsM3A1A@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Sergey Organov","fromEmail":"sorganov@gmail.com","sentAt":"2020-05-04T19:51:20Z","receivedAt":"2020-05-04T19:51:27Z","isPatch":false,"sender":{"key":"sorganov@gmail.com","avatar":"https://avatars.githubusercontent.com/u/8501568?v=4"},"body":"Ewa Śliwińska writes:\n\n> Hi Sergey,\n>\n> Thanks for engaging here.\n>\n> Actually, I gave some details in the first email, I'm not sure if they\n> were even noticed.\n>\n> About asking second time: I emphasized this because I felt this part\n> was ignored and I didn't like it.\n>\n> I wanted to describe problem more generally and gave you the commands.\n> But now I will paste the console full output as you demanded:\n>\n> mac:lp3rater noelo$ git status\n>\n> On branch master\n>\n> Your branch is based on 'origin/master', but the upstream is gone.\n>\n> (use \"git branch --unset-upstream\" to fixup)\n\nThis is something I've never seen before. Dunno how this happened to\nyou, but to me it rings a bell that something weird goes on in this\nrepo. Maybe it's in fact nothing, but then you may get all kinds of\nnasty behaviors if repo is indeed broken.\n\n>\n>\n> Changes to be committed:\n>\n> (use \"git reset HEAD ...\" to unstage)\n>\n>\n> new file: .idea/.gitignore\n[... a lot more new files ...]\n\nInteresting. Is it the .gitignore that tells git to ignore all files in\n.idea/? If so, it's not a good idea for .gitignore to ignore itself.\nIt's very confusing at minimum.\n\nMany new files also tells that you somehow, apparently by mistake, added\nall these files to staging (that will be committed at the next commit).\n\nAlso, apparently you already did this same thing before, so there are\nsome more files from .idea/ that are already there.\n\n[...]\n\n> Changes not staged for commit:\n>\n> (use \"git add ...\" to update what will be committed)\n>\n> (use \"git checkout -- ...\" to discard changes in working directory)\n>\n>\n> modified: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n> modified: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n> modified: .idea/sonarlint/issuestore/index.pb\n\nThese were likely already committed at the previous commit(s) and now\nhave some changes. Try, say:\n\n$ git log -- .idea/sonarlint/issuestore/index.pb\n\nto see what commit added the file.\n\nIn addition, try:\n\n$ git check-ignore .idea/sonarlint/issuestore/index.pb\n\nto check if the file you think is ignored is in fact ignored, as it'd be\nthe simplest explanation of your troubles if it isn't.\n\nHTH,\n-- Sergey\n"},{"id":"396978","messageId":"CAEoQP9ic7yU01JWkjiNT40gtq0WyUW7sBAJPRRdBRw93dhRw9w@mail.gmail.com","threadId":"53384","inReplyTo":"87o8r3cwcn.fsf@osv.gnss.ru","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-04T20:04:00Z","receivedAt":"2020-05-04T20:04:14Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"I don't know why would something be broken in my repo. As I wrote, I\nsimply clone it (empty) from bitbucket and than started adding code,\nreally nothing extraordinary.\n\n\"Is it the .gitignore that tells git to ignore all files in\n.idea/?\" - no, it contains some default-ignored by idea files.\nThe one that I'm using (or at least intended to) is on the main level.\n\nThis is the output of the commands you wrote me to run:\n\nmac:.idea noelo$ git log -- .idea/sonarlint/issuestore/index.pb\n\nmac:.idea noelo$ git check-ignore .idea/sonarlint/issuestore/index.pb\n\n.idea/sonarlint/issuestore/index.pb\n\nmac:.idea noelo$\n\nSo it still seems like the file was not committed and it is ignored as\nfar as I understand this.\n\nOn Mon, 4 May 2020 at 21:51, Sergey Organov wrote:\n>\n> Ewa Śliwińska writes:\n>\n> > Hi Sergey,\n> >\n> > Thanks for engaging here.\n> >\n> > Actually, I gave some details in the first email, I'm not sure if they\n> > were even noticed.\n> >\n> > About asking second time: I emphasized this because I felt this part\n> > was ignored and I didn't like it.\n> >\n> > I wanted to describe problem more generally and gave you the commands.\n> > But now I will paste the console full output as you demanded:\n> >\n> > mac:lp3rater noelo$ git status\n> >\n> > On branch master\n> >\n> > Your branch is based on 'origin/master', but the upstream is gone.\n> >\n> > (use \"git branch --unset-upstream\" to fixup)\n>\n> This is something I've never seen before. Dunno how this happened to\n> you, but to me it rings a bell that something weird goes on in this\n> repo. Maybe it's in fact nothing, but then you may get all kinds of\n> nasty behaviors if repo is indeed broken.\n>\n> >\n> >\n> > Changes to be committed:\n> >\n> > (use \"git reset HEAD ...\" to unstage)\n> >\n> >\n> > new file: .idea/.gitignore\n> [... a lot more new files ...]\n>\n> Interesting. Is it the .gitignore that tells git to ignore all files in\n> .idea/? If so, it's not a good idea for .gitignore to ignore itself.\n> It's very confusing at minimum.\n>\n> Many new files also tells that you somehow, apparently by mistake, added\n> all these files to staging (that will be committed at the next commit).\n>\n> Also, apparently you already did this same thing before, so there are\n> some more files from .idea/ that are already there.\n>\n> [...]\n>\n> > Changes not staged for commit:\n> >\n> > (use \"git add ...\" to update what will be committed)\n> >\n> > (use \"git checkout -- ...\" to discard changes in working directory)\n> >\n> >\n> > modified: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n> > modified: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n> > modified: .idea/sonarlint/issuestore/index.pb\n>\n> These were likely already committed at the previous commit(s) and now\n> have some changes. Try, say:\n>\n> $ git log -- .idea/sonarlint/issuestore/index.pb\n>\n> to see what commit added the file.\n>\n> In addition, try:\n>\n> $ git check-ignore .idea/sonarlint/issuestore/index.pb\n>\n> to check if the file you think is ignored is in fact ignored, as it'd be\n> the simplest explanation of your troubles if it isn't.\n>\n> HTH,\n> -- Sergey\n"},{"id":"396985","messageId":"871rnz4eln.fsf@igel.home","threadId":"53384","inReplyTo":"CAEoQP9guAWg8E95Pi4MOih7z5rPg7OCB+_jZ6EMhJxpFsM3A1A@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Andreas Schwab","fromEmail":"schwab@linux-m68k.org","sentAt":"2020-05-04T20:41:56Z","receivedAt":"2020-05-04T20:42:02Z","isPatch":false,"sender":{"key":"schwab@linux-m68k.org","avatar":"https://avatars.githubusercontent.com/u/2175493?v=4"},"body":"On Mai 04 2020, Ewa Śliwińska wrote:\n\n> Changes to be committed:\n>\n> (use \"git reset HEAD ...\" to unstage)\n>\n>\n> new file: .idea/.gitignore\n>\n> new file: .idea/compiler.xml\n>\n> new file: .idea/encodings.xml\n>\n> new file: .idea/jarRepositories.xml\n>\n> new file: .idea/libraries/Maven__commons_codec_commons_codec_1_11.xml\n>\n> new file: .idea/libraries/Maven__commons_io_commons_io_2_6.xml\n>\n> new file: .idea/libraries/Maven__commons_logging_commons_logging_1_2.xml\n>\n> new file: .idea/libraries/Maven__commons_net_commons_net_3_6.xml\n>\n> new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_2_39_1.xml\n>\n> new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_core_js_2_39_0.xml\n>\n> new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_cssparser_1_5_0.xml\n>\n> new file: .idea/libraries/Maven__net_sourceforge_htmlunit_neko_htmlunit_2_39_0.xml\n>\n> new file: .idea/libraries/Maven__org_apache_commons_commons_lang3_3_10.xml\n>\n> new file: .idea/libraries/Maven__org_apache_commons_commons_text_1_8.xml\n>\n> new file: .idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_5_12.xml\n>\n> new file: .idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_4_13.xml\n>\n> new file: .idea/libraries/Maven__org_apache_httpcomponents_httpmime_4_5_12.xml\n>\n> new file: .idea/libraries/Maven__org_brotli_dec_0_1_2.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_client_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_http_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_io_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_util_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_xml_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_api_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_client_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_common_9_4_27_v20200227.xml\n>\n> new file: .idea/libraries/Maven__xalan_serializer_2_7_2.xml\n>\n> new file: .idea/libraries/Maven__xalan_xalan_2_7_2.xml\n>\n> new file: .idea/libraries/Maven__xerces_xercesImpl_2_12_0.xml\n>\n> new file: .idea/libraries/Maven__xml_apis_xml_apis_1_4_01.xml\n>\n> new file: .idea/misc.xml\n>\n> new file: .idea/modules.xml\n>\n> new file: .idea/sonarlint/issuestore/2/2/22a598feccb13c958ecc8eff5c53a9a7f9470a72\n>\n> new file: .idea/sonarlint/issuestore/4/4/442292b8a7efeabbe4cc176709b833b1792140ec\n>\n> new file: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n>\n> new file: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n>\n> new file: .idea/sonarlint/issuestore/index.pb\n>\n> new file: .idea/vcs.xml\n\nThat means you have explicitly staged all these files with git add.\n\nAndreas.\n\n-- \nAndreas Schwab, schwab@linux-m68k.org\nGPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n\"And now for something completely different.\"\n"},{"id":"397059","messageId":"CAEoQP9jkP6KinqOM41zbJhV7+MbA742Xgit2ztK1OcJ78+YbdQ@mail.gmail.com","threadId":"53384","inReplyTo":"871rnz4eln.fsf@igel.home","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-05T07:49:11Z","receivedAt":"2020-05-05T07:49:24Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"Thank you, but those are not what I ask about here. I guess the Idea\nmust did it for me.\nThat is not the problem now, I worry only about those \"modified\" files.\n\nPozdrawiam\nEwa\n\n\nOn Mon, 4 May 2020 at 22:41, Andreas Schwab wrote:\n>\n> On Mai 04 2020, Ewa Śliwińska wrote:\n>\n> > Changes to be committed:\n> >\n> > (use \"git reset HEAD ...\" to unstage)\n> >\n> >\n> > new file: .idea/.gitignore\n> >\n> > new file: .idea/compiler.xml\n> >\n> > new file: .idea/encodings.xml\n> >\n> > new file: .idea/jarRepositories.xml\n> >\n> > new file: .idea/libraries/Maven__commons_codec_commons_codec_1_11.xml\n> >\n> > new file: .idea/libraries/Maven__commons_io_commons_io_2_6.xml\n> >\n> > new file: .idea/libraries/Maven__commons_logging_commons_logging_1_2.xml\n> >\n> > new file: .idea/libraries/Maven__commons_net_commons_net_3_6.xml\n> >\n> > new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_2_39_1.xml\n> >\n> > new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_core_js_2_39_0.xml\n> >\n> > new file: .idea/libraries/Maven__net_sourceforge_htmlunit_htmlunit_cssparser_1_5_0.xml\n> >\n> > new file: .idea/libraries/Maven__net_sourceforge_htmlunit_neko_htmlunit_2_39_0.xml\n> >\n> > new file: .idea/libraries/Maven__org_apache_commons_commons_lang3_3_10.xml\n> >\n> > new file: .idea/libraries/Maven__org_apache_commons_commons_text_1_8.xml\n> >\n> > new file: .idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_5_12.xml\n> >\n> > new file: .idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_4_13.xml\n> >\n> > new file: .idea/libraries/Maven__org_apache_httpcomponents_httpmime_4_5_12.xml\n> >\n> > new file: .idea/libraries/Maven__org_brotli_dec_0_1_2.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_client_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_http_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_io_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_util_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_jetty_xml_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_api_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_client_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__org_eclipse_jetty_websocket_websocket_common_9_4_27_v20200227.xml\n> >\n> > new file: .idea/libraries/Maven__xalan_serializer_2_7_2.xml\n> >\n> > new file: .idea/libraries/Maven__xalan_xalan_2_7_2.xml\n> >\n> > new file: .idea/libraries/Maven__xerces_xercesImpl_2_12_0.xml\n> >\n> > new file: .idea/libraries/Maven__xml_apis_xml_apis_1_4_01.xml\n> >\n> > new file: .idea/misc.xml\n> >\n> > new file: .idea/modules.xml\n> >\n> > new file: .idea/sonarlint/issuestore/2/2/22a598feccb13c958ecc8eff5c53a9a7f9470a72\n> >\n> > new file: .idea/sonarlint/issuestore/4/4/442292b8a7efeabbe4cc176709b833b1792140ec\n> >\n> > new file: .idea/sonarlint/issuestore/c/0/c02b58f69e810278d2d423bdee557628145ed943\n> >\n> > new file: .idea/sonarlint/issuestore/f/b/fb31951790c271e26d568f9ac5b7681e7f0804ec\n> >\n> > new file: .idea/sonarlint/issuestore/index.pb\n> >\n> > new file: .idea/vcs.xml\n>\n> That means you have explicitly staged all these files with git add.\n>\n> Andreas.\n>\n> --\n> Andreas Schwab, schwab@linux-m68k.org\n> GPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n> \"And now for something completely different.\"\n"},{"id":"397060","messageId":"87zhamiz3r.fsf@igel.home","threadId":"53384","inReplyTo":"CAEoQP9jkP6KinqOM41zbJhV7+MbA742Xgit2ztK1OcJ78+YbdQ@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Andreas Schwab","fromEmail":"schwab@linux-m68k.org","sentAt":"2020-05-05T08:07:36Z","receivedAt":"2020-05-05T08:07:41Z","isPatch":false,"sender":{"key":"schwab@linux-m68k.org","avatar":"https://avatars.githubusercontent.com/u/2175493?v=4"},"body":"On Mai 05 2020, Ewa Śliwińska wrote:\n\n> That is not the problem now, I worry only about those \"modified\" files.\n\nJust git add them again. Each time you git add a file, only the current\ncontent is staged. If you modify it further, you need to git add it\nagain if you want to commit the new contents.\n\nAndreas.\n\n-- \nAndreas Schwab, schwab@linux-m68k.org\nGPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n\"And now for something completely different.\"\n"},{"id":"397061","messageId":"CAEoQP9jvpCnC0Ag=xZVSpCE_CgyddLooSGi35NcMQf=0se3BEw@mail.gmail.com","threadId":"53384","inReplyTo":"87zhamiz3r.fsf@igel.home","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-05T08:10:58Z","receivedAt":"2020-05-05T08:11:12Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"We probably don't understand each other. At least I don't get you.\n\nI don't know what you think I want with them, but it's definitely not adding.\nAnd the problem is I would like to know what HAPPENED or why they are\ndisplaying as they were added when at the same time it seems they\nweren't (that was never my intention).\n\nOn Tue, 5 May 2020 at 10:07, Andreas Schwab wrote:\n>\n> On Mai 05 2020, Ewa Śliwińska wrote:\n>\n> > That is not the problem now, I worry only about those \"modified\" files.\n>\n> Just git add them again. Each time you git add a file, only the current\n> content is staged. If you modify it further, you need to git add it\n> again if you want to commit the new contents.\n>\n> Andreas.\n>\n> --\n> Andreas Schwab, schwab@linux-m68k.org\n> GPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n> \"And now for something completely different.\"\n"},{"id":"397062","messageId":"87v9laiysb.fsf@igel.home","threadId":"53384","inReplyTo":"CAEoQP9jvpCnC0Ag=xZVSpCE_CgyddLooSGi35NcMQf=0se3BEw@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Andreas Schwab","fromEmail":"schwab@linux-m68k.org","sentAt":"2020-05-05T08:14:28Z","receivedAt":"2020-05-05T08:14:32Z","isPatch":false,"sender":{"key":"schwab@linux-m68k.org","avatar":"https://avatars.githubusercontent.com/u/2175493?v=4"},"body":"On Mai 05 2020, Ewa Śliwińska wrote:\n\n> I don't know what you think I want with them, but it's definitely not adding.\n\nThen why did you stage them in the first place?\n\nAndreas.\n\n-- \nAndreas Schwab, schwab@linux-m68k.org\nGPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n\"And now for something completely different.\"\n"},{"id":"397063","messageId":"CAEoQP9iqSDRd27os1YDBmZ-YHGNcgDwztzmuOi3aSzK7DD9kFA@mail.gmail.com","threadId":"53384","inReplyTo":"87v9laiysb.fsf@igel.home","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-05T08:19:13Z","receivedAt":"2020-05-05T08:19:27Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"I didn't, not explicitly. Maybe my IDE, but I don't know how that happened.\nAnd first of all, I don't want to talk about those files at all. Just\nabout the modified ones below.\nDon't get me wrong, I can answer your questions, I just don't see how\nthis is relevant.\n\nOn Tue, 5 May 2020 at 10:14, Andreas Schwab wrote:\n>\n> On Mai 05 2020, Ewa Śliwińska wrote:\n>\n> > I don't know what you think I want with them, but it's definitely not adding.\n>\n> Then why did you stage them in the first place?\n>\n> Andreas.\n>\n> --\n> Andreas Schwab, schwab@linux-m68k.org\n> GPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n> \"And now for something completely different.\"\n"},{"id":"397064","messageId":"87r1vyiya4.fsf@igel.home","threadId":"53384","inReplyTo":"CAEoQP9iqSDRd27os1YDBmZ-YHGNcgDwztzmuOi3aSzK7DD9kFA@mail.gmail.com","subject":"Re: file is showing as modified even that it was never commited","fromName":"Andreas Schwab","fromEmail":"schwab@linux-m68k.org","sentAt":"2020-05-05T08:25:23Z","receivedAt":"2020-05-05T08:25:28Z","isPatch":false,"sender":{"key":"schwab@linux-m68k.org","avatar":"https://avatars.githubusercontent.com/u/2175493?v=4"},"body":"On Mai 05 2020, Ewa Śliwińska wrote:\n\n> And first of all, I don't want to talk about those files at all. Just\n> about the modified ones below.\n\nYou cannot ignore the staged files, that's the key to your confusion.\n\nAndreas.\n\n-- \nAndreas Schwab, schwab@linux-m68k.org\nGPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n\"And now for something completely different.\"\n"},{"id":"397065","messageId":"CAEoQP9j=oRDchdd=NLwUFJ1sHWxHY6rn9vRTdpCLOVD08q7SRA@mail.gmail.com","threadId":"53384","inReplyTo":"87r1vyiya4.fsf@igel.home","subject":"Re: file is showing as modified even that it was never commited","fromName":"Ewa Śliwińska","fromEmail":"kreska07@gmail.com","sentAt":"2020-05-05T08:34:04Z","receivedAt":"2020-05-05T08:34:17Z","isPatch":false,"sender":{"key":"kreska07@gmail.com","avatar":"https://gravatar.com/avatar/0691f2436f90d4f938cb0332a22e969bb9bd86b29ac2c8586a6bcf07d245af16?d=mp&s=160"},"body":"Wow, your completely right. Thanks a lot!\nNow I see they must have been somehow staged, then changed and only\nchanges are not staged... That explains everything.\n\nI don't know how I staged them now, and I guess you can't help me\nanswer this question, what is important is that they are in fact\nstaged.\n\nMaybe that's a problem with IDE or I did it somehow accidentally...\nAnyway, that seems explained now, not bug.\nThank you all a lot once again.\n\nOn Tue, 5 May 2020 at 10:25, Andreas Schwab wrote:\n>\n> On Mai 05 2020, Ewa Śliwińska wrote:\n>\n> > And first of all, I don't want to talk about those files at all. Just\n> > about the modified ones below.\n>\n> You cannot ignore the staged files, that's the key to your confusion.\n>\n> Andreas.\n>\n> --\n> Andreas Schwab, schwab@linux-m68k.org\n> GPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1\n> \"And now for something completely different.\"\n"}]}