This is the umpteenth version of the extremely basic question "why the heck is Git telling me that files changed but diff shows no changes?". Similar questions have been posted here and here but none of those answers help.
My scenario is as follows:
I added a .gitattributes file to an existing Git repo with several already existing commits in it. The content of the .gitattributes file looks as follows:
* text=auto
*.bat text eol=crlf
*.cmd text eol=crlf
*.ps1 text eol=crlf
*.sh text eol=lf
*.csproj text eol=crlf
*.filters text eol=crlf
*.props text eol=crlf
*.sqlproj text eol=crlf
*.sln text eol=crlf
*.vcxitems text eol=crlf
*.vcxproj text eol=crlf
*.cs text
*.config text
*.jmx text
*.json text
*.sql text
*.tt text
*.ttinclude text
*.wxi text
*.wxl text
*.wxs text
*.xaml text
*.xml text
*.bmp binary
*.gif binary
*.ico binary
*.jpg binary
*.pdf binary
*.png binary
After adding that file I executed the following command:
git rm --cached -r .
git reset --hard
The result is that Git git status now shows most of the files in the Git repo as modified. However, I cannot see any changes in any of those files. The diff tool isn't showing any changes, neither in the text view nor in its hex view.
The repo has been created on a Windows machine and I'm currently using it on a Windows machine. The output of the command git config --list is as follows:
http.sslbackend=schannel
diff.astextplain.textconv=astextplain
credential.helper=manager-core
core.autocrlf=true
core.fscache=true
core.symlinks=false
core.editor="C:\\Program Files\\Notepad++\\notepad++.exe" -multiInst -notabbar -nosession -noPlugin
pull.rebase=false
credential.https://dev.azure.com.usehttppath=true
init.defaultbranch=master
user.name=My Name
user.email=my#email.whatever
core.autocrlf=true
core.eol=crlf
diff.tool=bc
difftool.bc.path=C:/Program Files/Beyond Compare 4/bcomp.exe
difftool.bc.cmd="C:/Program Files/Beyond Compare 4/bcomp.exe" "$LOCAL" "$REMOTE"
difftool.bc.prompt=false
merge.tool=bc
mergetool.bc.path=C:/Program Files/Beyond Compare 4/bcomp.exe
mergetool.bc.cmd="C:/Program Files/Beyond Compare 4/bcomp.exe" "$LOCAL" "$REMOTE" "$BASE" "$MERGED"
mergetool.bc.keepbackup=false
mergetool.bc.trustexitcode=true
core.repositoryformatversion=0
core.filemode=false
core.bare=false
core.logallrefupdates=true
core.symlinks=false
core.ignorecase=true
So the magic switches core.autocrlf and core.eol are as they should be for Windows as far as I could decrypt from the documentation.
Does anyone have a clue what Git landmine I've stepped on here?
There are multiple possibilities here, but the most common by far has to do with these CRLF line endings. It's complicated, and to really get it, we need some background first.
From a high level point of view, Git basically has two options:
Don't mess with line endings ever.
Do mess with line endings.
The first one is really simple, and is the default on all Unix-like systems. It's probably the default on Windows too, but I don't use Windows, so I'd have to defer to anyone else who says otherwise. In this setup, if you create a file and store, in that file, the byte-sequence:
h e l l o CTRL-M CTRL-J w o r l d CTRL-M CTRL-J
and then git add the file and run git commit, Git will store, in the repository, a new commit in which that file contains those 14 bytes. The blob hash ID will be:
$ printf 'blob 14\0hello\r\nworld\r\n' | shasum
23eb407b644b0e362fa224168ecd0adfa02b022a
This file has CRLF line endings. Extracting the commit will produce a file with CRLF line endings. The file in the repository is now read-only, frozen for all time; it has blob hash ID 23eb407b644b0e362fa224168ecd0adfa02b022a, as does every file in any Git repository anywhere in the universe, as long as that file contains exactly that text.
Now suppose, having created this file (or not), we turn on the "do mess with line endings" options. We now get numerous sub-options, specifying just how Git will go about messing with line endings, when, on which files. These include eol=crlf, eol=lf, text, binary, and so on:
*.bat text eol=crlf
*.sh text eol=lf
*.jpg binary
This fragment tells Git that if the file's name ends with .bat, Git should mess with line endings in one particular way; if it ends with .sh, Git should mess with line endings in another particular way; and if it ends with .jpg, Git should not mess with line endings.
We know that the binary specification means that for such files, Git doesn't mess with line endings. This is good since, for instance, .jpg files do not actually have lines in the first place, so that anything that resembles a line ending is just coincidence. When Git isn't messing with anything, it's all easy: Git is storing what's there and showing you what's stored.
But that's no longer true for the other files. Since Git is now messing with their line endings, it becomes important to ask and answer more questions:
When exactly does Git mess with the line endings?
What exactly does Git do when it does this messing-about?
This is where things get complicated. The key to understanding things here is to know about Git's index. This thing—this "index"—is central in Git and you really do have to know about it to use Git properly, so let's take a tour of the index.
Git's index
Git's index is either so important or so poorly named (or both) that it actually has three names. It is also called the staging area, which refers to how you normally use it, and it is sometimes called the cache. This last name is pretty rare these days: you mostly see it in flags like git rm --cached. (Some commands, like git diff, have both --staged and --cached, with the same meaning. For some reason no one has gotten around to adding git rm --staged yet. I thought that would have happened by now, and I still think it will happen someday.)
The index does a bunch of things for Git, but here we really care about what it does for—and to—you. What it does for you is hold your proposed next commit. Git is, fundamentally, not about files, but rather about commits. Each commit holds files: in fact, each commit has a full snapshot of every file. (Each commit also has some metadata, such as the name and email address of the commit's author, but we'll skip that here.)
The thing about commits, though, is that they're purely read-only. You can make new ones, but you can never change any existing commit. The git commit --amend command, for instance, fakes it: it does not change the existing commit, it makes a new one and stops using the old one in favor of the new one instead. When you can't tell the difference—and sometimes you can't—this is just as good. When you can tell the difference—and sometimes you can—the cracks show through.
But if you can't change a commit—and you can't—and if, as is also true, the files inside a commit are in a special, compressed, de-duplicated, Git-only form that no programs other than Git itself can even read in the first place, how can you use the files that are inside a commit? The answer is simple enough: In order to use a commit, you have to have Git extract that commit first. We run git checkout or git switch to achieve this. Git extracts the files from the commit, placing usable version of them in our working tree or work-tree, where we can see them and get our work done.
Git could stop here, with committed files—read-only inside the current commit, frozen for all time—and working files. Other version control systems do stop here. But Git doesn't. Instead, as it's extracting the commit, Git puts "copies" of each file into Git's index.
I put "copies" in quotes here because the files in Git's index are stored in the internal, compressed, de-duplicated format. Since they were just extracted from some commit, they take no space: they're de-duplicated away. They hold the same data in the index that they hold when they're inside the commit: this data is frozen for all time.
What's special about the index "copies" of files is that, unlike the committed copies, you can replace them. The git add command tells Git: compress and de-duplicate the working tree file. Git reads the working tree copy, compresses it, and checks to see if the compressed result is a duplicate of some existing file in any existing commit. (This is where that blob hash ID trick comes in: it's why any file consisting entirely of hello\r\nworld\r\n has hash ID 23eb407b644b0e362fa224168ecd0adfa02b022a.) If this is a duplicate, Git puts the duplicate's hash ID in the index. If it's not a duplicate, Git arranges to store a new blob in the object database,1 and stores the new blob's hash ID in the index.
Either way, after this update-the-index step, the proposed next commit is now updated. The file you git add-ed is now staged, and git status will compare the staged hash ID to the current-commit hash ID and say staged for commit if these hash ID's don't match. (This means that git add-ing a file that's been turned back to match the committed copy takes away the staged for commit message, even though the file will in fact be in the next commit. It's just that the hash IDs now match!)
So, Git's index holds this proposed next commit. To make a new commit, you:
futz with the files in your working tree;
run git add on them to copy them back into Git's index; and
run git commit to package up whatever is in Git's index right then.
This is why you have to keep git adding a file each time you change it: Git doesn't automatically copy the working tree file back into the index. Git only copies it back when you say to do that.2
The end effect—and what you should take into the next section—is that, at all times, Git has three copies of each file:
HEAD index work-tree
--------- --------- ---------
README.md README.md README.md
img.jpg img.jpg img.jpg
main.py main.py main.py
for instance. The work-tree version is the one you can see, read, write, feed to a JPG viewer, run with the Python program, and so on. The other two are for Git: the HEAD version is the frozen-for-all-time copy from the current commit and the index version is the malleable-but-frozen-format copy, ready to go into the next commit.
The git checkout or git switch command switches to some commit, copying the files out of the commit to Git's index and then to your working tree.
The git restore command reads a file from somewhere—a commit or the index—and writes it to the index and/or your working tree based on the -S (write to staging) and -W (write to work-tree) options.
The git reset -- file command reads a file from Git's index and writes it to your working tree. (The -- here is a precaution, in case the name of the file is, say, master or dev or something that resembles a branch name).
The git add file command reads a file from your working tree and writes it to the index.
(Lots of alternatives are not listed here.)
So all these various commands are tricks for manipulating the index and/or working tree copy, in preparation for making the next commit (since Git is mostly about making new commits, while keeping all the old ones).
1Git actually stores the new compressed blob object immediately, even if it winds up being replaced before you make a new commit. This is okay (if perhaps sub-optimal in certain peculiar situations) because Git will run git gc for you now and then. Certain older Git versions had a bug where git gc didn't get run often enough, and this could actually be a problem, but that's been fixed for years now.
2Using git add -u tells Git to find modified working tree files, and add them, which automates the job. Using git commit -a is a lot like running git add -u && git commit: it runs a git add -u step before the commit. However, -a complicates things a bunch, and interacts badly with poorly-written pre-commit hooks, so it's kind of a bad idea. Try not to rely on it: use git add -u instead, in case you have one of these bad commit hooks. Or, learn to love the index, which lets you play clever tricks like git add -p, although this too interacts badly with poorly-written pre-commit hooks.
How and when Git messes with line endings
If:
Git is told to mess with line endings, and
a file is marked text, so that Git will mess with this file, or the text=auto setting is being used and Git guesses that this file is text
then:
Git will optionally mess with the file's bytes on the way from index to working tree (checkout or switch, restore, various kinds of reset, etc), and
Git will mess with the file's bytes on the way from working tree to index (add, mostly).
What messing-about will Git do? That depends on the eol= setting:
eol=crlf: On the way out, Git will change LF-only to CRLF. If a line reads hello\n in the index, Git will write hello\r\n to the working tree copy. On the way in, Git will change CRLF to LF-only. If a line reads hello\r\n in the working tree copy, Git will write hello\n to the index copy.
eol=lf: On the way out, Git will do nothing to the file. On the way in, Git will change CRLF to LF-only.
That's it—that's all Git will do! It won't ever change LF to CRLF on the way in, for instance. In that sense, we could say that Git "prefers" LF-only line endings. (If you want something fancier, you can write clean and smudge filters, which also operate on data "on the way in" and "on the way out" respectively, and here you can do whatever you like. But the built in stuff inside Git is limited to these few CRLF options.)
There's one more tricky bit: Git tries hard to optimize not making copies, in or out, of the index and working tree. This attempt usually works right, but it fails (by not making copies when it should make copies) if and when you switch around whether and how Git should mess with line endings. The tricks you linked to, where you rm .git/index for instance, are mostly ways to get around this. This forces Git to copy data, even in cases where Git thinks it doesn't need to copy data, even though the changed status of a file (from -text to text, or eol=lf to eol=crlf, or whatever) means that Git does have to copy.
This is all that you need to memorize. The remaining details can be worked out.
Consequences
Suppose you have a repository in which, in every commit that has text files, all committed copies have LF-only line endings. Since this is, in effect, Git's "preferred" format, the files are already all "OK". If you choose to have Git mess with files, all future commits will have LF-only line endings too, and the future commits will match the existing commits.
But suppose you have a repository in which some or all text files are committed with CRLF line endings. These commits are frozen for all time! You literally cannot change them. They will continue to have CRLF line endings. If you now begin choosing to have Git mess with files, future commits will gradually, or suddenly all at once, have some or all files with LF-only line endings, as stored in the repository.
Regardless of which of the above statements about the existing repository are true, your settings, should you set them, will affect how you see the files in your working tree, because to get into your working tree, Git has to extract the files from commits. But your file viewers might not show you what the ends of lines look like. That is, if your preferred file viewer displays a CRLF line and an LF-only line as identical, they'll look identical, even when they aren't.
The fact that the ends of lines "change" can make a change that Git considers a change. If the existing commits in the repository have CRLF line endings, and you start having Git mess with line endings, it's a good idea to do one "normalizing" commit. You will become the owner of every line of every file that is changed this way but git blame, at least, has a way to "skip over" a specific commit, if you need to figure out where some code came from. Since this "fix all files, but no real changes" commit doesn't do anything except normalize these lines, you can tell git blame to skip over it.
Note that Git (and git diff) do consider these lines different, unless you tell git diff to ignore certain white space changes:
--ignore-cr-at-eol: Ignore carriage-return at the end of line when doing a comparison.
-w, --ignore-all-space: Ignore whitespace when comparing lines.
(There are others; this is just a partial list.)
Other items that should be mentioned here
When Git commits a file, it stores both the file's data and its "mode". Git has two modes for files, which it calls 100644 and 100755 when it shows them, but for which git update-index has a --chmod option that it spells -x and +x respectively. This tells Git that on a Unix-like system or any other system that has an equivalent, the 100755 or +x file should be marked executable at checkout.
Most Windows file systems currently don't have an equivalent. In this case, Git tries to retain the chmod setting from the existing checkout. The rm .git/index trick defeats this "retain the old setting" trick. So it's possible to change the mode of files when fixing end-of-line issues. This is why it's better to use git add --renormalize after changing CRLF line endings settings, if your Git supports this.
The general idea that there are some changes, or features of files, that are invisible or hard to see is a little weird, but we have non-computing examples: for instance, in fine typesetting, we have the hyphen (-), the en-dash (–), and the em-dash (—). These may or may not display on your computer as different width dashes. We have other computer examples, such as the Whitespace programming language or the terrible mistake with makefile syntax (where tabs are significant). And, in spycraft—whether or not we use computers—we have steganography.
Our team works on repository which includes one directory where there are files with pipe character "|". I'm the only one on Windows so pipe character is illegal for files names.
Is there a way to rename files in the directory "extra" from ex. "2021|08|05" to "2021\08\05" when I make "git pull"?
Is there a way to rename files in the directory "extra" from ex. "2021\08\05" to "2021|08|05" when I make "git push"?
No.
No.
These are the right answers to the question you've asked, but the trick is, you've asked the wrong question. Alas, the answer to the right question is: "yes, but it's a horrible solution". The question is: Is there a solution to the problem of bad / invalid characters in file names stored in Git commits?
In the early days of Git, when it was a collection of shell scripts that only a few people could use successfully, 😀 one would obtain new commits from elsewhere with git fetch, then read these commits into Git's index with git read-tree.
Git's index, which Git also calls the staging area or sometimes the cache, can hold these file names. In fact, even on Windows, Git's index can hold files named aux.h, which Windows won't let you create. The index has no folders either: it just has files with names with embedded (forward) slashes, such as path/to/file. Git can hold two different files, one named README and one named readme, in its index. WIndows can't have two different files whose name only differs in case.
So, Git's index / staging-area can hold these files just fine. The problem comes when you go to work with the files. Files that are in Git's index, are stored there in a special Git-only format, as what Git calls a blob object. You cannot read or write a blob object directly. You have to use yet more Git commands to do this. It's terribly inconvenient.
To use Git conveniently, then, we normally don't use all the individual one-step-at-a-time internal Git operations: we use some sort of higher level, user oriented command, like git checkout. We check out an entire commit: Git will find all the files that are stored in that commit, read them into Git's index, and copy out and expand all the internal Git-only blob objects into ordinary files, with ordinary file names.
This step—copying files out of Git's index, to make them usable—is where things go wrong, on Windows. The file's name in Git's index is, say, path/to/2021|08|05. Git recognizes that path/to/ has to be turned into two folders, path\ and path\to\, on Windows, so that Git can create a a file in the second folder. Unfortunately, Git has no way to remap the 2021|08|05 part. That part is going to stay 2021|08|05, and as you have seen, Git can't create a file with that name: the OS just says "no".
What you can do, at this point, is drop down to those lower-level commands. You can run:
git rev-parse :path/to/2021|08|05
perhaps with quotes if needed, depending on your shell:
git rev-parse ":path/to/2021|08|05"
This git rev-parse command will show the blob hash ID for the file. You can then access the file's contents with:
git cat-file -p <hash>
which prints those contents to the standard output. If your shell supports redirection, you can then redirect the output to a file whose name is your choice. This lets you see and use the file's contents.
The git cat-file -p command can take the index path name directly, so:
git cat-file -p ":path/to/2021|08|05" > path/to/2021-08-05
is a way to extract the file to a usable name.
Unfortunately, git add—which is how you would normally update the file—will insist on using the name you gave the file in the file system. Once again, you must fall back on internal Git plumbing commands to work around this. If you need to update that particular file, for instance, you would:
run git hash-object -w -t blob path/to/2021-08-05 to turn the updated file's data into an internal Git object;
run git update-index with arguments to make Git update the entry for path/to/2021|08|05 using the hash ID obtained in step 1.
Once all of this is done, you can go back to normal Git commands, because git commit makes a new commit from what's in Git's index / staging-area.
The (rather large) drawback here is that you cannot use a lot of normal everyday Git commands:
git pull is often a no-go because it runs git rebase or git merge, both of which need to use your working tree (OS-level files). Run git fetch first, then do as much manual work as needed.
git checkout will fail: you can use it, but then you must manually do something about each of the bad file names that are now in Git's index.
git diff will show differences that include deleting the files with the bad names, and git status will show the adjusted-name files as untracked files (because they are).
git add of any changes you need to make to these files is also a no-go; use git hash-object -w and git update-index instead.
git rebase and git merge become difficult. You probably can deal with them as in steps 2 and 4, but that's painful at best.
I recently discovered that there are a couple folders in my solution that have two distinct paths in Git (GitHub shows two separate folders), one being FooBar and the other being Foobar. This is because some files were registered with the former folder name as their path, and some with the latter.
This was discovered locally (in Windows) by configuring Git to not ignore case: git config core.ignorecase false
I took a stab at fixing this by deleting the whole folder, committing, then re-adding the folder and committing again. This fixed the problem, but the files that got their paths changed lost their Git History. Running gitk against the new path for these files showed just the one commit. Running gitk against their old path revealed their whole history.
Next stab: Use git mv to move the file:
git mv Foobar/file.txt FooBar/file.txt
This yields the error:
fatal: destination exists, source=Foobar/file.txt, destination=FooBar/file.txt
And if I try deleting the file first, of course Git complains that the source file doesn't exist.
Then I discovered Git doesn't complain about the destination already existing if you add -f to the mv command. However, after committing that rename, gitk shows that the history got severed anyway!
I even attempted to do the three step dance described here but this was just another way of doing the -f. Same result.
Basically I just want to move a file from Foobar/file.txt to FooBar/file.txt in a case-insensitive operating system in some way, while preserving Git history. Is this possible?
There is no simple solution to the real problem.
In Git, files don't have history. Commits have history—or more precisely, commits are the history. That is all the history there is. For Git to "follow" a file, as in git log --follow <path>, Git looks at the commits, one at a time, comparing each commit to its parent commit.
If a diff between parent and child shows that the parent contains a file named parent/path/to/pfile and the child contains a file named child/path/to/cfile and the content of these two files, in these two commits, is "sufficiently similar" (several conditions must hold here), then, in Git's "eyes", that parent-to-child transition represents a rename of that file. So at that point, git log --follow, which had been looking for child/path/to/cfile, starts looking instead for parent/path/to/pfile.
Without --follow, git log does not do this special "find a rename" operation ... and in general, Git believes that any path names with any byte-level difference represent different files. In other words, case-folding and UTF-8 normalization do not occur. Consider, e.g., the word schön, which can be represented as either s c h ö n or s c h o combining-¨ n. We can, on a Linux box, create two different files using these two different UTF-8 style names. Running ls will show two files whose name appears the same:
$ cat umlaut.py
import os
p1 = u'sch\N{latin small letter o with diaeresis}n'
p2 = u'scho\N{combining diaeresis}n'
os.close(os.open(p1.encode('utf8'), os.O_CREAT, 0o666))
os.close(os.open(p2.encode('utf8'), os.O_CREAT, 0o666))
$ python umlaut.py
$ ls
schön schön umlaut.py
Git is perfectly happy to store both files, separately. However, MacOS refuses to allow both files to coexist, in the same way that Windows—and for that matter, MacOS by default as well—refuses to allow both Foobar and FooBar to coexist.
Make Git store the file in new commits under the new byte-sequence, and history is preserved, it's just not the history you want preserved. But the history that's already in the repository is already not the history you want preserved.
In practice, you should probably just rename the file in Git's eyes—which has no effect on the file's name in your OS's eyes; FooBar and Foobar are the same name here—and get on with things. Your alternative is to rewrite all history going back in time to the point at which the bad pairings were first added to the repository, by copying (with slight modifications) each "bad" commit to a new-and-improved "good" commit. But this then means getting everyone who uses the repo to switch from "bad old repo" to "new and improved good repo".
I use git on windows. In my project I changed case of filename. After that checkout of previous commits failed (commands are in Git Bash):
mkdir repofolder
cd repofolder
git init # create empty repo
git config core.ignorecase false # turn on case-dependent filenames
# create 'readme.txt'
$ echo "blahblahblah" > readme.txt
$ git add readme.txt
$ git commit -m "+readme.txt"
# rename it to 'README.txt'
$ git mv -f readme.txt README.txt
$ git commit -m "readme.txt => README.txt"
$ git status
On branch master
nothing to commit, working directory clean
$ git checkout HEAD~1
error: The following untracked working tree files would be overwritten by checkout:
readme.txt
Please move or remove them before you can switch branches.
Aborting
Why git doesn't allow to checkout previos commits?
You face with the same problem when delete one file and append another one with the same name, but different case. No matter how many commits you do: one (removing and appending in the same commit) or two commits (in first commit you remove file, in second you add another one).
On Windows git can't handle files with the same name but in different case properly
Git on Windows can't handle it because Windows itself can't handle it (emphasis mine):
As part of the requirements for POSIX compliance, the Windows NT File System (NTFS) provides a case-sensitive file and directory naming convention. Even though NTFS and the POSIX subsystem each handle case-sensitivity well, 16-bit Windows-based, MS-DOS-based, OS/2-based, and Win32-based applications do not.
In truth, Windows does have some level of support for NTFS case-sensitivity, but it's pretty flaky:
However, if you attempt to open one of these files in a Win32 application, such as Notepad, you would only have access to one of the files, regardless of the case of the filename you type in the Open File dialog box.
Other inconsistencies also exist. The Windows NT Command Prompt and File Manager correctly display the names of the files. However, normal commands, such as COPY, fail when you attempt to access one or more filenames that differ only in case.
I use TortoiseGit 1.8.3.
I changed one of the files: Makefile, but I want to not offer commit it to me every once in a Git Commit.
I added it to the "delete and add to ignore list", but it does not help.
How do I make to some of the files that I have changed is not offered in the commit?
I want, that Makefile was in remote repository as read-only, that I could edit it locally, and then TortoiseGit does not offer to me to commit it.
That I wanted for Git-bash: https://www.kernel.org/pub/software/scm/git/docs/git-update-index.html
Answer for TortoiseGit 1.8.15, Git 2.6.1. There is no need to revert to the command line, all functions are directly available in TortoiseGit. I've tried to summarize the various ways how this function is accessible.
I assume that the reader knows what "assume unchanged" means. Here is easy documentation about this feature. Or the original documentation about --assume-unchanged or git ls-files.
Flag a file as "assume unchanged"
There are three possibilities in TortoiseGit: in the Commit dialog, the Working Tree dialog (Check for Modifications) or in the Log Messages dialog (only when Working dir changes entry is selected). From one of these dialogs do the following:
right-click the file and select the entry Assume Unchanged
From any file list in Windows Explorer do the following:
right-click the file and select properties
go to the Git tab
tick the entry Assume valid/unchanged
Remove the "assume unchanged" flag from a file (undo the above):
TortoiseGit allows to remove the flag only from the Working Tree dialog (check for Modifications).
in the lower left corner of the dialog: make sure to tick the option Show ignore local changeds flagged files
all files with assumed valid or skip worktree flag will be shown below the normal changed files
right-click on the file and select Unflag as skip-worktree or assume-unchanged
From any file list in Windows Explorer do the following:
right-click the file and select properties
go to the Git tab
untick the entry Assume valid/unchanged
If I'm interpreting the question correctly, Alex wants to know how to undo an --assumed-unchanged action done using Tortoise Git.
You don't need to use command line Git to fix this:
Navigate to the file(s) you did this action on in windows explorer,
Right-click and choose Properties,
Select the Git tab, there you should see a checked box next to "Assume valid/unchanged".
Uncheck it and it won't be ignored by commits moving forward.
The approved answer is good but in case you're hunting for the dialogues and options here you have a short help:
If it doesn't help, then you need to go to a command-line interface, and check:
the content of the .gitignore file that you should find at the root directory of your repo (as mentioned in "TortoiseGit: hide/remove files never to be versioned")
the result of git rm --cached Makefile.
the result of git status.
I want, that Makefile was in remote repository in read-only, that I could edit it localy, and then TortoiseGIT does not offer to me to commit it.
This is different:
You need:
git update-index --really-refresh --no-assume-unchanged Makefile
That will make any local modification to Makefile "invisible" to git, while keeping Makefile under source control.
If you want your local modifs to resist a git reset, do;
git update-index --skip-worktree Makefile